Title: | Analysis of Large Affymetrix Microarray Data Sets |
---|---|
Description: | A cross-platform R framework that facilitates processing of any number of Affymetrix microarray samples regardless of computer system. The only parameter that limits the number of chips that can be processed is the amount of available disk space. The Aroma Framework has successfully been used in studies to process tens of thousands of arrays. This package has actively been used since 2006. |
Authors: | Henrik Bengtsson [aut, cre, cph], James Bullard [ctb], Kasper Hansen [ctb], Pierre Neuvial [ctb], Elizabeth Purdom [ctb], Mark Robinson [ctb], Ken Simpson [ctb] |
Maintainer: | Henrik Bengtsson <[email protected]> |
License: | LGPL (>= 2.1) |
Version: | 3.2.2 |
Built: | 2024-08-16 04:22:20 UTC |
Source: | https://github.com/HenrikBengtsson/aroma.affymetrix |
A cross-platform R framework that facilitates processing of any number of Affymetrix microarray samples regardless of computer system. The only parameter that limits the number of chips that can be processed is the amount of available disk space. The Aroma Framework has successfully been used in studies to process tens of thousands of arrays. This package has actively been used since 2006.
The preferred way to install this package is:
source("https://callr.org/install#aroma.affymetrix")
To get started, see the online user guides and the vignettes https://www.aroma-project.org/.
In order to keep improving and providing support for this project, please cite references [1], [2], or any applicable publication listed on https://aroma-project.org/publications/, whenever you publish work that have been used any of the Aroma Framework.
The releases of this package is licensed under LGPL version 2.1 or newer.
The development code of the packages is under a private license (where applicable) and patches sent to the author fall under the latter license, but will be, if incorporated, released under the "release" license above.
Henrik Bengtsson, James Bullard, Kasper Hansen, Pierre Neuvial, Elizabeth Purdom, Mark Robinson, Ken Simpson
[1] H. Bengtsson, K. Simpson, J. Bullard, and K. Hansen, aroma.affymetrix: A generic framework in R for analyzing small to very large Affymetrix data sets in bounded memory, Tech Report #745, Department of Statistics, University of California, Berkeley, February 2008.
[2] H. Bengtsson, R. Irizarry, B. Carvalho, and T. Speed, Estimation and assessment of raw copy numbers at the single locus level, Bioinformatics, 2008.
[3] H. Bengtsson, The R.oo package - Object-Oriented Programming with References Using Standard R Code, In Kurt Hornik, Friedrich Leisch and Achim Zeileis, editors, Proceedings of the 3rd International Workshop on Distributed Statistical Computing (DSC 2003), March 20-22, Vienna, Austria. https://www.r-project.org/conferences/DSC-2003/Proceedings/
For a complete list, see https://aroma-project.org/publications/.
Package: aroma.affymetrix
Class AbstractProbeSequenceNormalization
Object
~~|
~~+--
ParametersInterface
~~~~~~~|
~~~~~~~+--
AromaTransform
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
Transform
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
ProbeLevelTransform
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
ProbeLevelTransform3
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AbstractProbeSequenceNormalization
Directly known subclasses:
BaseCountNormalization, BasePositionNormalization, LinearModelProbeSequenceNormalization, MatNormalization
public abstract static class AbstractProbeSequenceNormalization
extends ProbeLevelTransform3
This abstract class represents a normalization method that corrects for systematic effects in the probe intensities due to differences in probe sequences.
AbstractProbeSequenceNormalization(..., target=NULL)
AbstractProbeSequenceNormalization(..., target=NULL)
... |
Arguments passed to the constructor of
|
target |
A |
Methods:
getTargetFile |
- | |
process |
- | |
Methods inherited from ProbeLevelTransform3:
getAsteriskTags, getCellsTo, getCellsToFit, getCellsToUpdate, getParameters, getUnitsTo, getUnitsToFit, getUnitsToUpdate, writeSignals
Methods inherited from ProbeLevelTransform:
getRootPath
Methods inherited from Transform:
getOutputDataSet, getOutputFiles
Methods inherited from AromaTransform:
as.character, findFilesTodo, getAsteriskTags, getExpectedOutputFiles, getExpectedOutputFullnames, getFullName, getInputDataSet, getName, getOutputDataSet, getOutputDataSet0, getOutputFiles, getPath, getRootPath, getTags, isDone, process, setTags
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
This class requires that an AromaCellSequenceFile
is
available for the chip type.
Henrik Bengtsson
Package: aroma.affymetrix
Class AdditiveCovariatesNormalization
Object
~~|
~~+--
ParametersInterface
~~~~~~~|
~~~~~~~+--
AromaTransform
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
Transform
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
ChipEffectTransform
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
AdditiveCovariatesNormalization
Directly known subclasses:
GcContentNormalization2
public abstract static class AdditiveCovariatesNormalization
extends ChipEffectTransform
This class represents a normalization method that corrects for GC-content effects on copy-number chip-effect estimates.
AdditiveCovariatesNormalization(dataSet=NULL, ..., target=NULL, subsetToFit="-XY", shift=0, onMissing=c("median", "ignore"))
AdditiveCovariatesNormalization(dataSet=NULL, ..., target=NULL, subsetToFit="-XY", shift=0, onMissing=c("median", "ignore"))
dataSet |
|
... |
Additional arguments passed to the constructor of
|
target |
(Optional) A |
subsetToFit |
The units from which the normalization curve should
be estimated. If |
onMissing |
Specifies how to normalize units for which the GC contents are unknown. |
shift |
An optional amount the data points should be shifted (translated). |
For SNPs, the normalization function is estimated based on the total chip effects, i.e. the sum of the allele signals. The normalizing is done by rescale the chip effects on the intensity scale such that the mean of the total chip effects are the same across samples for any given GC content. For allele-specific estimates, both alleles are always rescaled by the same amount. Thus, when normalizing allele-specific chip effects, the total chip effects is change, but not the relative allele signal, e.g. the allele B frequency.
Methods:
getCdf |
- | |
process |
- | |
Methods inherited from ChipEffectTransform:
getRootPath
Methods inherited from Transform:
getOutputDataSet, getOutputFiles
Methods inherited from AromaTransform:
as.character, findFilesTodo, getAsteriskTags, getExpectedOutputFiles, getExpectedOutputFullnames, getFullName, getInputDataSet, getName, getOutputDataSet, getOutputDataSet0, getOutputFiles, getPath, getRootPath, getTags, isDone, process, setTags
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.affymetrix
Class AffineCnPlm
Object
~~|
~~+--
ParametersInterface
~~~~~~~|
~~~~~~~+--
Model
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
UnitModel
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
MultiArrayUnitModel
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
ProbeLevelModel
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AffinePlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AffineSnpPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
SnpPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
CnPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AffineCnPlm
Directly known subclasses:
public abstract static class AffineCnPlm
extends CnPlm
AffineCnPlm(..., combineAlleles=FALSE)
AffineCnPlm(..., combineAlleles=FALSE)
... |
Arguments passed to |
combineAlleles |
If |
Methods:
No methods defined.
Methods inherited from CnPlm:
getCellIndices, getChipEffectSet, getCombineAlleles, getParameters, getProbeAffinityFile, setCombineAlleles
Methods inherited from SnpPlm:
getCellIndices, getChipEffectSet, getMergeStrands, getParameters, getProbeAffinityFile, setMergeStrands
Methods inherited from AffineSnpPlm:
getAsteriskTags
Methods inherited from AffinePlm:
getAsteriskTags, getFitUnitGroupFunction, getProbeAffinityFile
Methods inherited from ProbeLevelModel:
calculateResidualSet, calculateWeights, fit, getAsteriskTags, getCalculateResidualsFunction, getChipEffectSet, getProbeAffinityFile, getResidualSet, getRootPath, getWeightsSet
Methods inherited from MultiArrayUnitModel:
getListOfPriors, setListOfPriors, validate
Methods inherited from UnitModel:
findUnitsTodo, getAsteriskTags, getFitSingleCellUnitFunction, getParameters
Methods inherited from Model:
as.character, fit, getAlias, getAsteriskTags, getDataSet, getFullName, getName, getPath, getRootPath, getTags, setAlias, setTags
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.affymetrix
Class AffinePlm
Object
~~|
~~+--
ParametersInterface
~~~~~~~|
~~~~~~~+--
Model
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
UnitModel
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
MultiArrayUnitModel
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
ProbeLevelModel
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AffinePlm
Directly known subclasses:
AffineCnPlm, AffineSnpPlm
public abstract static class AffinePlm
extends ProbeLevelModel
This class represents affine model in Bengtsson & Hossjer (2006).
AffinePlm(..., background=TRUE)
AffinePlm(..., background=TRUE)
... |
Arguments passed to |
background |
If |
Methods:
getProbeAffinityFile |
- | |
Methods inherited from ProbeLevelModel:
calculateResidualSet, calculateWeights, fit, getAsteriskTags, getCalculateResidualsFunction, getChipEffectSet, getProbeAffinityFile, getResidualSet, getRootPath, getWeightsSet
Methods inherited from MultiArrayUnitModel:
getListOfPriors, setListOfPriors, validate
Methods inherited from UnitModel:
findUnitsTodo, getAsteriskTags, getFitSingleCellUnitFunction, getParameters
Methods inherited from Model:
as.character, fit, getAlias, getAsteriskTags, getDataSet, getFullName, getName, getPath, getRootPath, getTags, setAlias, setTags
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
For a single unit group, the affine model is:
where is an offset common to all probe signals,
are the chip effects for arrays
,
and
are the probe affinities for probes
.
The
are zero-mean noise with equal variance.
The model is constrained such that
.
Note that with the additional constraint (see arguments above),
the above model is very similar to
MbeiPlm
. The differences in
parameter estimates is due to difference is assumptions about the
error structure, which in turn affects how the model is estimated.
Henrik Bengtsson
Bengtsson & Hossjer (2006).
Package: aroma.affymetrix
Class AffineSnpPlm
Object
~~|
~~+--
ParametersInterface
~~~~~~~|
~~~~~~~+--
Model
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
UnitModel
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
MultiArrayUnitModel
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
ProbeLevelModel
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AffinePlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
SnpPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AffineSnpPlm
Directly known subclasses:
AffineCnPlm
public abstract static class AffineSnpPlm
extends SnpPlm
AffineSnpPlm(..., mergeStrands=FALSE)
AffineSnpPlm(..., mergeStrands=FALSE)
... |
Arguments passed to |
mergeStrands |
If |
Methods:
No methods defined.
Methods inherited from SnpPlm:
getCellIndices, getChipEffectSet, getMergeStrands, getParameters, getProbeAffinityFile, setMergeStrands
Methods inherited from AffinePlm:
getAsteriskTags, getFitUnitGroupFunction, getProbeAffinityFile
Methods inherited from ProbeLevelModel:
calculateResidualSet, calculateWeights, fit, getAsteriskTags, getCalculateResidualsFunction, getChipEffectSet, getProbeAffinityFile, getResidualSet, getRootPath, getWeightsSet
Methods inherited from MultiArrayUnitModel:
getListOfPriors, setListOfPriors, validate
Methods inherited from UnitModel:
findUnitsTodo, getAsteriskTags, getFitSingleCellUnitFunction, getParameters
Methods inherited from Model:
as.character, fit, getAlias, getAsteriskTags, getDataSet, getFullName, getName, getPath, getRootPath, getTags, setAlias, setTags
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.affymetrix
Class AffymetrixCdfFile
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
CacheKeyInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
AromaMicroarrayDataFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaChipTypeAnnotationFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
UnitAnnotationDataFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
UnitTypesFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
UnitNamesFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixCdfFile
Directly known subclasses:
public abstract static class AffymetrixCdfFile
extends UnitNamesFile
An AffymetrixCdfFile object represents a generic Affymetrix CDF file.
AffymetrixCdfFile(...)
AffymetrixCdfFile(...)
... |
Arguments passed to |
Methods:
convert |
- | |
createExonByTranscriptCdf |
- | |
getACSFile |
- | |
getAromaCellSequenceFile |
- | |
getCellIndices |
- | |
getChipType |
- | |
getDimension |
- | |
getFileFormat |
- | |
getGenomeInformation |
- | |
getImage |
- | |
getPlatform |
- | |
getUnitNames |
- | |
getUnitTypes |
- | |
hasUnitTypes |
- | |
isMonocellCdf |
- | |
isPm |
- | |
isUniqueCdf |
- | |
nbrOfCells |
- | |
nbrOfColumns |
- | |
nbrOfQcUnits |
- | |
nbrOfRows |
- | |
nbrOfUnits |
- | |
readDataFrame |
- | |
readUnits |
- | |
Methods inherited from UnitNamesFile:
getUnitNames, indexOf, nbrOfUnits
Methods inherited from UnitTypesFile:
getUnitTypes, nbrOfUnits
Methods inherited from UnitAnnotationDataFile:
byChipType, getAromaUflFile, getAromaUgpFile, getChipType, getDefaultExtension, getPlatform, nbrOfUnits
Methods inherited from AromaPlatformInterface:
getAromaPlatform, getAromaUflFile, getAromaUgpFile, getChipType, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith
Methods inherited from AromaChipTypeAnnotationFile:
as.character, byChipType, byName, findByChipType, fromFile, getChipType, getDefaultExtension, getHeader, getPlatform
Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags
Methods inherited from FileCacheKeyInterface:
getCacheKey
Methods inherited from CacheKeyInterface:
getCacheKey
Methods inherited from GenericDataFile:
as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson, Ken Simpson
Package: aroma.affymetrix
Class AffymetrixCelFile
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
CacheKeyInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
AromaMicroarrayDataFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixCelFile
Directly known subclasses:
ChipEffectFile, CnChipEffectFile, CnProbeAffinityFile, ExonChipEffectFile, ExonProbeAffinityFile, FirmaFile, ParameterCelFile, ProbeAffinityFile, QualityAssessmentFile, ResidualFile, SnpChipEffectFile, SnpProbeAffinityFile, WeightsFile
public abstract static class AffymetrixCelFile
extends AffymetrixFile
An AffymetrixCelFile object represents a single Affymetrix CEL file.
AffymetrixCelFile(..., cdf=NULL)
AffymetrixCelFile(..., cdf=NULL)
... |
Arguments passed to |
cdf |
An optional |
Methods:
extractMatrix |
- | |
getAm |
- | |
getCdf |
- | |
getFileFormat |
- | |
getImage |
- | |
getUnitNamesFile |
- | |
getUnitTypesFile |
- | |
image270 |
- | |
nbrOfCells |
- | |
plotDensity |
- | |
plotImage |
- | |
plotMvsA |
- | |
plotMvsX |
- | |
setCdf |
- | |
smoothScatterMvsA |
- | |
writeImage |
- | |
Methods inherited from AromaPlatformInterface:
getAromaPlatform, getAromaUflFile, getAromaUgpFile, getChipType, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith
Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags
Methods inherited from FileCacheKeyInterface:
getCacheKey
Methods inherited from CacheKeyInterface:
getCacheKey
Methods inherited from GenericDataFile:
as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
If you subclass this class, please make sure to query the
AffymetrixCdfFile
object (see *getCdf()
) whenever
querying CDF information. Do not use the CDF file inferred from the
chip type in CEL header, unless you really want it to be hardwired that
way, otherwise you will break to possibility to override the CDF
structure.
Henrik Bengtsson
An object of this class is typically part of an AffymetrixCelSet
.
Package: aroma.affymetrix
Class AffymetrixCelSet
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFileSet
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
AromaMicroarrayDataSet
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixFileSet
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixCelSet
Directly known subclasses:
ChipEffectSet, CnChipEffectSet, ExonChipEffectSet, FirmaSet, ParameterCelSet, QualityAssessmentSet, ResidualSet, SnpChipEffectSet, WeightsSet
public static class AffymetrixCelSet
extends AffymetrixFileSet
An AffymetrixCelSet object represents a set of Affymetrix CEL files with identical chip types.
AffymetrixCelSet(files=NULL, ...)
AffymetrixCelSet(files=NULL, ...)
files |
A |
... |
Not used. |
Methods:
as |
- | |
as.AffymetrixCelSet |
- | |
byName |
- | |
doCRMAv1 |
- | |
doCRMAv2 |
- | |
doFIRMA |
- | |
doGCRMA |
- | |
doRMA |
- | |
extractAffyBatch |
- | |
extractFeatureSet |
- | |
extractMatrix |
- | |
getAverage |
- | |
getAverageAsinh |
- | |
getAverageFile |
- | |
getAverageLog |
- | |
getCdf |
- | |
getChipType |
- | |
getData |
- | |
getIntensities |
- | |
getPlatform |
- | |
getTimestamps |
- | |
getUnitGroupCellMap |
- | |
getUnitIntensities |
- | |
getUnitNamesFile |
- | |
getUnitTypesFile |
- | |
justSNPRMA |
- | |
plotDensity |
- | |
readUnits |
- | |
setCdf |
- | |
writeSgr |
- | |
Methods inherited from AffymetrixFileSet:
as, as.AffymetrixFileSet, byPath, getDefaultFullName
Methods inherited from AromaPlatformInterface:
getAromaPlatform, getAromaUflFile, getAromaUgpFile, getChipType, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith
Methods inherited from AromaMicroarrayDataSet:
as.AromaMicroarrayDataSetList, as.AromaMicroarrayDataSetTuple, getAromaFullNameTranslatorSet, getAverageFile, getChipType, getDefaultFullName, getPlatform, setAttributesBy, setAttributesBySampleAnnotationFile, setAttributesBySampleAnnotationSet, validate
Methods inherited from GenericDataFileSet:
[, [[, anyDuplicated, anyNA, append, appendFiles, appendFullNamesTranslator, appendFullNamesTranslatorByNULL, appendFullNamesTranslatorByTabularTextFile, appendFullNamesTranslatorByTabularTextFileSet, appendFullNamesTranslatorBydata.frame, appendFullNamesTranslatorByfunction, appendFullNamesTranslatorBylist, as.character, as.list, byName, byPath, c, clearCache, clearFullNamesTranslator, clone, copyTo, dsApplyInPairs, duplicated, equals, extract, findByName, findDuplicated, getChecksum, getChecksumFileSet, getChecksumObjects, getDefaultFullName, getFile, getFileClass, getFileSize, getFiles, getFullNames, getNames, getOneFile, getPath, getPathnames, getSubdirs, gunzip, gzip, hasFile, indexOf, is.na, names, nbrOfFiles, rep, resetFullNames, setFullNamesTranslator, sortBy, unique, update2, updateFullName, updateFullNames, validate, getFullNameTranslatorSet, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
## Not run: for (zzz in 0) { # Find any dataset path <- NULL if (is.null(path)) break # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Define a dataset object based on all CEL files in a directory # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ds <- AffymetrixCelSet$fromFiles(path) print(ds) # Keep at most three arrays for this example ds <- ds[1:min(3,nbrOfArrays(ds))] print(ds) } # for (zzz in 0) rm(zzz) ## End(Not run)
## Not run: for (zzz in 0) { # Find any dataset path <- NULL if (is.null(path)) break # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Define a dataset object based on all CEL files in a directory # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ds <- AffymetrixCelSet$fromFiles(path) print(ds) # Keep at most three arrays for this example ds <- ds[1:min(3,nbrOfArrays(ds))] print(ds) } # for (zzz in 0) rm(zzz) ## End(Not run)
Package: aroma.affymetrix
Class AffymetrixCelSetReporter
Object
~~|
~~+--
GenericReporter
~~~~~~~|
~~~~~~~+--
AffymetrixFileSetReporter
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
AffymetrixCelSetReporter
Directly known subclasses:
SpatialReporter
public abstract static class AffymetrixCelSetReporter
extends AffymetrixFileSetReporter
AffymetrixCelSetReporter(..., .setClass="AffymetrixCelSet")
AffymetrixCelSetReporter(..., .setClass="AffymetrixCelSet")
... |
Arguments passed to |
.setClass |
The name of the class of the input set. |
Methods:
getDataSet |
- | |
Methods inherited from AffymetrixFileSetReporter:
getFileSet, getInputName, getInputTags
Methods inherited from GenericReporter:
as.character, getAlias, getAsteriskTags, getFullName, getInputName, getInputTags, getMainPath, getName, getPath, getReportSet, getRootPath, getTags, process, setAlias, setup
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.affymetrix
Class AffymetrixCelSetTuple
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFileSetList
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
AromaMicroarrayDataSetTuple
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
AffymetrixCelSetTuple
Directly known subclasses:
ChipEffectSetTuple, CnChipEffectSetTuple
public static class AffymetrixCelSetTuple
extends AromaMicroarrayDataSetTuple
AffymetrixCelSetTuple(..., .setClass="AffymetrixCelSet")
AffymetrixCelSetTuple(..., .setClass="AffymetrixCelSet")
... |
Arguments passed to the constructor of
|
.setClass |
The name of the class of the input set. |
Methods:
byPath |
- | |
Methods inherited from AromaMicroarrayDataSetTuple:
as, as.AromaMicroarrayDataSetTuple, byPath, getAsteriskTags, getChipTypes, getFullNames, getSets, getTags, indexOf, nbrOfChipTypes
Methods inherited from GenericDataFileSetList:
as, as.GenericDataFileSetList, as.character, as.data.frame, as.list, assertDuplicates, clone, extract, getAsteriskTags, getDefaultFullName, getFileList, getFileListClass, getFullNames, getNames, getSet, getSets, getTags, indexOf, length, nbrOfFiles, nbrOfSets, setTags
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.affymetrix
Class AffymetrixCnChpSet
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFileSet
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
AromaMicroarrayDataSet
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixFileSet
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixCnChpSet
Directly known subclasses:
public abstract static class AffymetrixCnChpSet
extends AffymetrixFileSet
A AffymetrixCnChpSet object represents a set of AffymetrixCnChpFile:s with identical chip types.
AffymetrixCnChpSet(files=NULL, ...)
AffymetrixCnChpSet(files=NULL, ...)
files |
A |
... |
Not used. |
Methods:
as |
- | |
as.AffymetrixCnChpSet |
- | |
exportTotalCnRatioSet |
- | |
extractLogRatios |
- | |
findByName |
- | |
getCdf |
- | |
setCdf |
- | |
Methods inherited from AffymetrixFileSet:
as, as.AffymetrixFileSet, byPath, getDefaultFullName
Methods inherited from AromaPlatformInterface:
getAromaPlatform, getAromaUflFile, getAromaUgpFile, getChipType, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith
Methods inherited from AromaMicroarrayDataSet:
as.AromaMicroarrayDataSetList, as.AromaMicroarrayDataSetTuple, getAromaFullNameTranslatorSet, getAverageFile, getChipType, getDefaultFullName, getPlatform, setAttributesBy, setAttributesBySampleAnnotationFile, setAttributesBySampleAnnotationSet, validate
Methods inherited from GenericDataFileSet:
[, [[, anyDuplicated, anyNA, append, appendFiles, appendFullNamesTranslator, appendFullNamesTranslatorByNULL, appendFullNamesTranslatorByTabularTextFile, appendFullNamesTranslatorByTabularTextFileSet, appendFullNamesTranslatorBydata.frame, appendFullNamesTranslatorByfunction, appendFullNamesTranslatorBylist, as.character, as.list, byName, byPath, c, clearCache, clearFullNamesTranslator, clone, copyTo, dsApplyInPairs, duplicated, equals, extract, findByName, findDuplicated, getChecksum, getChecksumFileSet, getChecksumObjects, getDefaultFullName, getFile, getFileClass, getFileSize, getFiles, getFullNames, getNames, getOneFile, getPath, getPathnames, getSubdirs, gunzip, gzip, hasFile, indexOf, is.na, names, nbrOfFiles, rep, resetFullNames, setFullNamesTranslator, sortBy, unique, update2, updateFullName, updateFullNames, validate, getFullNameTranslatorSet, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.affymetrix
Class AffymetrixFile
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
CacheKeyInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
AromaMicroarrayDataFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixFile
Directly known subclasses:
AffymetrixCdfFile, AffymetrixCelFile, AffymetrixCnChpFile, AffymetrixPgfFile, AffymetrixTsvFile, AromaChipTypeAnnotationFile, ChipEffectFile, CnChipEffectFile, CnProbeAffinityFile, CnagCfhFile, DChipCdfBinFile, DChipDcpFile, ExonChipEffectFile, ExonProbeAffinityFile, FirmaFile, ParameterCelFile, ProbeAffinityFile, QualityAssessmentFile, ResidualFile, SnpChipEffectFile, SnpProbeAffinityFile, WeightsFile
public abstract static class AffymetrixFile
extends AromaPlatformInterface
An AffymetrixFile object represents a single Affymetrix file,
e.g. an Affymetrix CEL file or an Affymetrix CDF file.
Note that this class is abstract and can not be instanciated, but
instead you have to use one of the subclasses or the generic
fromFile()
method.
AffymetrixFile(...)
AffymetrixFile(...)
... |
Arguments passed to |
Methods:
No methods defined.
Methods inherited from AromaPlatformInterface:
getAromaPlatform, getAromaUflFile, getAromaUgpFile, getChipType, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith
Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags
Methods inherited from FileCacheKeyInterface:
getCacheKey
Methods inherited from CacheKeyInterface:
getCacheKey
Methods inherited from GenericDataFile:
as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
An object of this class is typically part of an AffymetrixFileSet
.
Package: aroma.affymetrix
Class AffymetrixFileSet
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFileSet
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
AromaMicroarrayDataSet
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixFileSet
Directly known subclasses:
AffymetrixCelSet, AffymetrixCnChpSet, ChipEffectSet, CnChipEffectSet, DChipDcpSet, ExonChipEffectSet, FirmaSet, ParameterCelSet, QualityAssessmentSet, ResidualSet, SnpChipEffectSet, WeightsSet
public abstract static class AffymetrixFileSet
extends AromaPlatformInterface
An AffymetrixFileSet object represents a set of AffymetrixFile
s
with identical chip types.
AffymetrixFileSet(files=NULL, ...)
AffymetrixFileSet(files=NULL, ...)
files |
A |
... |
Arguments passed to |
Methods:
as |
- | |
as.AffymetrixFileSet |
- | |
byPath |
- | |
Methods inherited from AromaPlatformInterface:
getAromaPlatform, getAromaUflFile, getAromaUgpFile, getChipType, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith
Methods inherited from AromaMicroarrayDataSet:
as.AromaMicroarrayDataSetList, as.AromaMicroarrayDataSetTuple, getAromaFullNameTranslatorSet, getAverageFile, getChipType, getDefaultFullName, getPlatform, setAttributesBy, setAttributesBySampleAnnotationFile, setAttributesBySampleAnnotationSet, validate
Methods inherited from GenericDataFileSet:
[, [[, anyDuplicated, anyNA, append, appendFiles, appendFullNamesTranslator, appendFullNamesTranslatorByNULL, appendFullNamesTranslatorByTabularTextFile, appendFullNamesTranslatorByTabularTextFileSet, appendFullNamesTranslatorBydata.frame, appendFullNamesTranslatorByfunction, appendFullNamesTranslatorBylist, as.character, as.list, byName, byPath, c, clearCache, clearFullNamesTranslator, clone, copyTo, dsApplyInPairs, duplicated, equals, extract, findByName, findDuplicated, getChecksum, getChecksumFileSet, getChecksumObjects, getDefaultFullName, getFile, getFileClass, getFileSize, getFiles, getFullNames, getNames, getOneFile, getPath, getPathnames, getSubdirs, gunzip, gzip, hasFile, indexOf, is.na, names, nbrOfFiles, rep, resetFullNames, setFullNamesTranslator, sortBy, unique, update2, updateFullName, updateFullNames, validate, getFullNameTranslatorSet, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.affymetrix
Class AffymetrixFileSetReporter
Object
~~|
~~+--
GenericReporter
~~~~~~~|
~~~~~~~+--
AffymetrixFileSetReporter
Directly known subclasses:
AffymetrixCelSetReporter, SpatialReporter
public abstract static class AffymetrixFileSetReporter
extends GenericReporter
AffymetrixFileSetReporter(set=NULL, ..., .setClass="AffymetrixFileSet")
AffymetrixFileSetReporter(set=NULL, ..., .setClass="AffymetrixFileSet")
set |
An |
... |
Arguments passed to |
.setClass |
The name of the class of the input set. |
Methods:
getInputName |
- | |
getInputTags |
- | |
Methods inherited from GenericReporter:
as.character, getAlias, getAsteriskTags, getFullName, getInputName, getInputTags, getMainPath, getName, getPath, getReportSet, getRootPath, getTags, process, setAlias, setup
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.affymetrix
Class AffymetrixPgfFile
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
CacheKeyInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
AromaMicroarrayDataFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaChipTypeAnnotationFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
UnitAnnotationDataFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
UnitTypesFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
UnitNamesFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixPgfFile
Directly known subclasses:
public abstract static class AffymetrixPgfFile
extends UnitNamesFile
An AffymetrixPgfFile object represents a generic Affymetrix Probe Group File (PGF). A PGF file "provides information about what probes are contained within a probeset and information about the nature of the probes necessary for analysis. The current PGF file format (version 1) is only specified for expression style probesets." [1]
AffymetrixPgfFile(...)
AffymetrixPgfFile(...)
... |
Arguments passed to |
Methods:
getChipType |
- | |
getDimension |
- | |
getPlatform |
- | |
getUnitNames |
- | |
nbrOfCells |
- | |
nbrOfColumns |
- | |
nbrOfRows |
- | |
nbrOfUnits |
- | |
Methods inherited from UnitNamesFile:
getUnitNames, indexOf, nbrOfUnits
Methods inherited from UnitTypesFile:
getUnitTypes, nbrOfUnits
Methods inherited from UnitAnnotationDataFile:
byChipType, getAromaUflFile, getAromaUgpFile, getChipType, getDefaultExtension, getPlatform, nbrOfUnits
Methods inherited from AromaPlatformInterface:
getAromaPlatform, getAromaUflFile, getAromaUgpFile, getChipType, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith
Methods inherited from AromaChipTypeAnnotationFile:
as.character, byChipType, byName, findByChipType, fromFile, getChipType, getDefaultExtension, getHeader, getPlatform
Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags
Methods inherited from FileCacheKeyInterface:
getCacheKey
Methods inherited from CacheKeyInterface:
getCacheKey
Methods inherited from GenericDataFile:
as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
[1] ...
Package: aroma.affymetrix
Class AlleleSummation
Object
~~|
~~+--
ParametersInterface
~~~~~~~|
~~~~~~~+--
Model
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
UnitModel
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
AlleleSummation
Directly known subclasses:
public abstract static class AlleleSummation
extends UnitModel
This class takes allele-specific chip effect estimates of a SnpChipEffectSet and returns a CnChipEffectSet holding the summed allele estimates.
AlleleSummation(dataSet=NULL, ignoreNAs=TRUE, ...)
AlleleSummation(dataSet=NULL, ignoreNAs=TRUE, ...)
dataSet |
|
ignoreNAs |
If |
... |
Arguments passed to |
Methods:
findUnitsTodo |
- | |
getChipEffectSet |
- | |
process |
- | |
Methods inherited from UnitModel:
findUnitsTodo, getAsteriskTags, getFitSingleCellUnitFunction, getParameters
Methods inherited from Model:
as.character, fit, getAlias, getAsteriskTags, getDataSet, getFullName, getName, getPath, getRootPath, getTags, setAlias, setTags
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.affymetrix
Class AllelicCrosstalkCalibration
Object
~~|
~~+--
ParametersInterface
~~~~~~~|
~~~~~~~+--
AromaTransform
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
Transform
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
ProbeLevelTransform
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
AllelicCrosstalkCalibration
Directly known subclasses:
public static class AllelicCrosstalkCalibration
extends ProbeLevelTransform
This class represents a calibration function that transforms the probe-level signals such that the signals from the two alleles are orthogonal. The method fits and calibrates PM signals only. MM signals will not affect the model fitting and are unaffected.
AllelicCrosstalkCalibration(dataSet=NULL, ..., model=c("asis", "auto", "CRMA", "CRMAv2"), rescaleBy=c("auto", "groups", "all", "none"), targetAvg=c(2200, 2200), subsetToAvg="-XY", mergeShifts=TRUE, B=1, flavor=c("sfit", "expectile"), alpha=c(0.1, 0.075, 0.05, 0.03, 0.01), q=2, Q=98, lambda=2, pairBy=c("CDF", "sequence"))
AllelicCrosstalkCalibration(dataSet=NULL, ..., model=c("asis", "auto", "CRMA", "CRMAv2"), rescaleBy=c("auto", "groups", "all", "none"), targetAvg=c(2200, 2200), subsetToAvg="-XY", mergeShifts=TRUE, B=1, flavor=c("sfit", "expectile"), alpha=c(0.1, 0.075, 0.05, 0.03, 0.01), q=2, Q=98, lambda=2, pairBy=c("CDF", "sequence"))
dataSet |
An |
... |
Arguments passed to the constructor of
|
model |
A |
rescaleBy |
A |
targetAvg |
The signal(s) that either the average of the sum
(if one target value) or the average of each of the alleles
(if two target values) should have after calibration.
Only used if |
subsetToAvg |
The indices of the cells (taken as the intersect of
existing indices) used to calculate average in order to rescale to
the target average. If |
mergeShifts |
If |
B |
An |
flavor |
A |
alpha , q , Q , lambda
|
Model fitting parameters. |
pairBy |
A |
Calibration for crosstalk between allele signals applies by definition only SNP units. Furthermore, it is only SNP units with two or four unit groups that are calibrated. For instance, in at least on custom SNP CDFs we know of, there is a small number of SNP units that have six groups. Currently these units are not calibrated (at all). It is only PM probes that will be calibrated. Note that, non-calibrated signals will be saved in the output files.
All PM probe pairs are used to fit the crosstalk model. In the second step where signals are rescaled to a target average, it is possible to specify the set of cells that should be included when estimating the target average.
Rescaling each allele-pair group (e.g. AC, AG, AT, CG, CT, GC)
towards a target average (rescaleBy="groups"
)
must not be used for multi-enzyme chip types,
e.g. GenomeWideSNP_6.
If still done, due to confounded effects of non-perfect enzyme
mixtures etc, there will be a significant bias between raw CNs
for SNPs and CN probes.
Instead, for such chip types all probe signals should be
rescale together towards the target average (rescaleBy="all"
).
Methods:
process |
- | |
Methods inherited from ProbeLevelTransform:
getRootPath
Methods inherited from Transform:
getOutputDataSet, getOutputFiles
Methods inherited from AromaTransform:
as.character, findFilesTodo, getAsteriskTags, getExpectedOutputFiles, getExpectedOutputFullnames, getFullName, getInputDataSet, getName, getOutputDataSet, getOutputDataSet0, getOutputFiles, getPath, getRootPath, getTags, isDone, process, setTags
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.affymetrix
Class AromaChipTypeAnnotationFile
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
CacheKeyInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
AromaMicroarrayDataFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaChipTypeAnnotationFile
Directly known subclasses:
AffymetrixCdfFile, AffymetrixPgfFile
public abstract static class AromaChipTypeAnnotationFile
extends AffymetrixFile
An AromaChipTypeAnnotationFile object represents an annotation file for a specific chip type.
AromaChipTypeAnnotationFile(...)
AromaChipTypeAnnotationFile(...)
... |
Arguments passed to |
Methods:
byChipType |
- | |
getChipType |
- | |
getHeader |
- | |
getPlatform |
- | |
Methods inherited from AromaPlatformInterface:
getAromaPlatform, getAromaUflFile, getAromaUgpFile, getChipType, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith
Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags
Methods inherited from FileCacheKeyInterface:
getCacheKey
Methods inherited from CacheKeyInterface:
getCacheKey
Methods inherited from GenericDataFile:
as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.affymetrix
Class ArrayExplorer
Object
~~|
~~+--
Explorer
~~~~~~~|
~~~~~~~+--
ArrayExplorer
Directly known subclasses:
public abstract static class ArrayExplorer
extends Explorer
ArrayExplorer(csTuple=NULL, ...)
ArrayExplorer(csTuple=NULL, ...)
csTuple |
An |
... |
Not used. |
Methods:
addColorMap |
- | |
getColorMaps |
- | |
getDataSet |
- | |
getSetTuple |
- | |
nbrOfChipTypes |
- | |
process |
- | |
setArrays |
- | |
setColorMaps |
- | |
Methods inherited from Explorer:
addIncludes, addIndexFile, as.character, display, getAlias, getArraysOfInput, getAsteriskTags, getFullName, getIncludePath, getMainPath, getName, getNameOfInput, getNames, getPath, getReportPathPattern, getRootPath, getSampleLayerPrefix, getSubname, getTags, getTagsOfInput, getTemplatePath, getVersion, nbrOfArrays, process, setAlias, setArrays, setReportPathPattern, setSubname, setup, splitByReportPathPattern, updateSetupExplorerFile
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.affymetrix
Class AvgCnPlm
Object
~~|
~~+--
ParametersInterface
~~~~~~~|
~~~~~~~+--
Model
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
UnitModel
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
MultiArrayUnitModel
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
ProbeLevelModel
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AvgPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AvgSnpPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
SnpPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
CnPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AvgCnPlm
Directly known subclasses:
public abstract static class AvgCnPlm
extends CnPlm
AvgCnPlm(..., combineAlleles=FALSE)
AvgCnPlm(..., combineAlleles=FALSE)
... |
Arguments passed to |
combineAlleles |
If |
Methods:
No methods defined.
Methods inherited from CnPlm:
getCellIndices, getChipEffectSet, getCombineAlleles, getParameters, getProbeAffinityFile, setCombineAlleles
Methods inherited from SnpPlm:
getCellIndices, getChipEffectSet, getMergeStrands, getParameters, getProbeAffinityFile, setMergeStrands
Methods inherited from AvgSnpPlm:
getAsteriskTags
Methods inherited from AvgPlm:
getAsteriskTags, getCalculateResidualsFunction, getParameters, validate
Methods inherited from ProbeLevelModel:
calculateResidualSet, calculateWeights, fit, getAsteriskTags, getCalculateResidualsFunction, getChipEffectSet, getProbeAffinityFile, getResidualSet, getRootPath, getWeightsSet
Methods inherited from MultiArrayUnitModel:
getListOfPriors, setListOfPriors, validate
Methods inherited from UnitModel:
findUnitsTodo, getAsteriskTags, getFitSingleCellUnitFunction, getParameters
Methods inherited from Model:
as.character, fit, getAlias, getAsteriskTags, getDataSet, getFullName, getName, getPath, getRootPath, getTags, setAlias, setTags
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.affymetrix
Class AvgPlm
Object
~~|
~~+--
ParametersInterface
~~~~~~~|
~~~~~~~+--
Model
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
UnitModel
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
MultiArrayUnitModel
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
ProbeLevelModel
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AvgPlm
Directly known subclasses:
AvgCnPlm, AvgSnpPlm
public abstract static class AvgPlm
extends ProbeLevelModel
This class represents a PLM where the probe intensities are averaged assuming identical probe affinities. For instance, one may assume that replicated probes with identical sequences have the same probe affinities, cf. the GenomeWideSNP_6 chip type.
AvgPlm(..., flavor=c("median", "mean"))
AvgPlm(..., flavor=c("median", "mean"))
... |
Arguments passed to |
flavor |
A |
Methods:
No methods defined.
Methods inherited from ProbeLevelModel:
calculateResidualSet, calculateWeights, fit, getAsteriskTags, getCalculateResidualsFunction, getChipEffectSet, getProbeAffinityFile, getResidualSet, getRootPath, getWeightsSet
Methods inherited from MultiArrayUnitModel:
getListOfPriors, setListOfPriors, validate
Methods inherited from UnitModel:
findUnitsTodo, getAsteriskTags, getFitSingleCellUnitFunction, getParameters
Methods inherited from Model:
as.character, fit, getAlias, getAsteriskTags, getDataSet, getFullName, getName, getPath, getRootPath, getTags, setAlias, setTags
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
For a single unit group, the averaging PLM of K probes is:
where are the chip effects for arrays
.
The
are zero-mean noise with equal variance.
The above model can be fitted in two ways, either robustly or
non-robustly.
Use argument flavor="mean"
to fit the model non-robustly, i.e.
.
Use argument flavor="median"
to fit the model robustly, i.e.
.
Missing values are always excluded.
Henrik Bengtsson
Package: aroma.affymetrix
Class AvgSnpPlm
Object
~~|
~~+--
ParametersInterface
~~~~~~~|
~~~~~~~+--
Model
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
UnitModel
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
MultiArrayUnitModel
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
ProbeLevelModel
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AvgPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
SnpPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AvgSnpPlm
Directly known subclasses:
AvgCnPlm
public abstract static class AvgSnpPlm
extends SnpPlm
AvgSnpPlm(..., mergeStrands=FALSE)
AvgSnpPlm(..., mergeStrands=FALSE)
... |
Arguments passed to |
mergeStrands |
If |
Methods:
No methods defined.
Methods inherited from SnpPlm:
getCellIndices, getChipEffectSet, getMergeStrands, getParameters, getProbeAffinityFile, setMergeStrands
Methods inherited from AvgPlm:
getAsteriskTags, getCalculateResidualsFunction, getParameters, validate
Methods inherited from ProbeLevelModel:
calculateResidualSet, calculateWeights, fit, getAsteriskTags, getCalculateResidualsFunction, getChipEffectSet, getProbeAffinityFile, getResidualSet, getRootPath, getWeightsSet
Methods inherited from MultiArrayUnitModel:
getListOfPriors, setListOfPriors, validate
Methods inherited from UnitModel:
findUnitsTodo, getAsteriskTags, getFitSingleCellUnitFunction, getParameters
Methods inherited from Model:
as.character, fit, getAlias, getAsteriskTags, getDataSet, getFullName, getName, getPath, getRootPath, getTags, setAlias, setTags
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.affymetrix
Class BackgroundCorrection
Object
~~|
~~+--
ParametersInterface
~~~~~~~|
~~~~~~~+--
AromaTransform
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
Transform
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
ProbeLevelTransform
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
BackgroundCorrection
Directly known subclasses:
GcRmaBackgroundCorrection, LimmaBackgroundCorrection, NormExpBackgroundCorrection, OpticalBackgroundCorrection, RmaBackgroundCorrection
public abstract static class BackgroundCorrection
extends ProbeLevelTransform
This class represents a background adjustment function.
BackgroundCorrection(..., subsetToUpdate=NULL, typesToUpdate=NULL)
BackgroundCorrection(..., subsetToUpdate=NULL, typesToUpdate=NULL)
... |
Arguments passed to the constructor of
|
subsetToUpdate |
The probes to be updated.
If |
typesToUpdate |
Types of probes to be updated. |
Methods:
process |
- | |
Methods inherited from ProbeLevelTransform:
getRootPath
Methods inherited from Transform:
getOutputDataSet, getOutputFiles
Methods inherited from AromaTransform:
as.character, findFilesTodo, getAsteriskTags, getExpectedOutputFiles, getExpectedOutputFullnames, getFullName, getInputDataSet, getName, getOutputDataSet, getOutputDataSet0, getOutputFiles, getPath, getRootPath, getTags, isDone, process, setTags
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Ken Simpson, Henrik Bengtsson
Package: aroma.affymetrix
Class BaseCountNormalization
Object
~~|
~~+--
ParametersInterface
~~~~~~~|
~~~~~~~+--
AromaTransform
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
Transform
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
ProbeLevelTransform
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
ProbeLevelTransform3
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AbstractProbeSequenceNormalization
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
BaseCountNormalization
Directly known subclasses:
public static class BaseCountNormalization
extends AbstractProbeSequenceNormalization
This class represents a normalization method that corrects for systematic effects in the probe intensities due to differences in the number of A, C, G, and T:s in the probe sequences.
BaseCountNormalization(..., model=c("robustSmoothSpline", "lm"), bootstrap=FALSE)
BaseCountNormalization(..., model=c("robustSmoothSpline", "lm"), bootstrap=FALSE)
... |
Arguments passed to the constructor of
|
model |
A |
bootstrap |
If |
Methods:
No methods defined.
Methods inherited from AbstractProbeSequenceNormalization:
fitOne, getAromaCellSequenceFile, getParameters, getTargetFile, indexOfMissingSequences, predictOne, process
Methods inherited from ProbeLevelTransform3:
getAsteriskTags, getCellsTo, getCellsToFit, getCellsToUpdate, getParameters, getUnitsTo, getUnitsToFit, getUnitsToUpdate, writeSignals
Methods inherited from ProbeLevelTransform:
getRootPath
Methods inherited from Transform:
getOutputDataSet, getOutputFiles
Methods inherited from AromaTransform:
as.character, findFilesTodo, getAsteriskTags, getExpectedOutputFiles, getExpectedOutputFullnames, getFullName, getInputDataSet, getName, getOutputDataSet, getOutputDataSet0, getOutputFiles, getPath, getRootPath, getTags, isDone, process, setTags
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
This class requires that an aroma probe sequence file is available for the chip type.
Henrik Bengtsson
Package: aroma.affymetrix
Class BasePositionNormalization
Object
~~|
~~+--
ParametersInterface
~~~~~~~|
~~~~~~~+--
AromaTransform
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
Transform
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
ProbeLevelTransform
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
ProbeLevelTransform3
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AbstractProbeSequenceNormalization
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
LinearModelProbeSequenceNormalization
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
BasePositionNormalization
Directly known subclasses:
public abstract static class BasePositionNormalization
extends LinearModelProbeSequenceNormalization
This class represents a normalization method that corrects for systematic effects in the probe intensities due to differences in positioning of A, C, G, and T:s in the probe sequences.
BasePositionNormalization(..., model=c("smooth.spline"), df=5)
BasePositionNormalization(..., model=c("smooth.spline"), df=5)
... |
Arguments passed to the constructor of
|
model |
A |
df |
The degrees of freedom of the model. |
Methods:
No methods defined.
Methods inherited from LinearModelProbeSequenceNormalization:
fitOne, getDesignMatrix, getNormalEquations, getSignalTransform, predictOne
Methods inherited from AbstractProbeSequenceNormalization:
fitOne, getAromaCellSequenceFile, getParameters, getTargetFile, indexOfMissingSequences, predictOne, process
Methods inherited from ProbeLevelTransform3:
getAsteriskTags, getCellsTo, getCellsToFit, getCellsToUpdate, getParameters, getUnitsTo, getUnitsToFit, getUnitsToUpdate, writeSignals
Methods inherited from ProbeLevelTransform:
getRootPath
Methods inherited from Transform:
getOutputDataSet, getOutputFiles
Methods inherited from AromaTransform:
as.character, findFilesTodo, getAsteriskTags, getExpectedOutputFiles, getExpectedOutputFullnames, getFullName, getInputDataSet, getName, getOutputDataSet, getOutputDataSet0, getOutputFiles, getPath, getRootPath, getTags, isDone, process, setTags
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson, Mark Robinson
Package: aroma.affymetrix
Class ChipEffectFile
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
CacheKeyInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
AromaMicroarrayDataFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixCelFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
ParametersInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
ParameterCelFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
ChipEffectFile
Directly known subclasses:
CnChipEffectFile, ExonChipEffectFile, SnpChipEffectFile
public abstract static class ChipEffectFile
extends ParameterCelFile
This class represents estimates of chip effects in the probe-level models.
ChipEffectFile(..., probeModel=c("pm"))
ChipEffectFile(..., probeModel=c("pm"))
... |
Arguments passed to |
probeModel |
The specific type of model, e.g. |
Methods:
extractMatrix |
- | |
extractTheta |
- | |
findUnitsTodo |
- | |
getAM |
- | |
readUnits |
- | |
Methods inherited from ParameterCelFile:
extractDataFrame, extractMatrix, readUnits
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from AffymetrixCelFile:
allocateFromCdf, as.character, clone, createFrom, extractMatrix, fromFile, getAm, getCdf, getExtensionPattern, getFileFormat, getImage, getUnitNamesFile, getUnitTypesFile, highlight, image270, nbrOfCells, plotDensity, plotImage, plotMvsA, plotMvsX, range, setCdf, smoothScatterMvsA, writeImage
Methods inherited from AromaPlatformInterface:
getAromaPlatform, getAromaUflFile, getAromaUgpFile, getChipType, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith
Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags
Methods inherited from FileCacheKeyInterface:
getCacheKey
Methods inherited from CacheKeyInterface:
getCacheKey
Methods inherited from GenericDataFile:
as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
An object of this class is typically obtained through the
getChipEffectSet()
method for the ProbeLevelModel
class.
An object of this class is typically part of a ChipEffectSet
.
Package: aroma.affymetrix
Class ChipEffectSet
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFileSet
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
AromaMicroarrayDataSet
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixFileSet
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixCelSet
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
ParametersInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
ParameterCelSet
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
ChipEffectSet
Directly known subclasses:
CnChipEffectSet, ExonChipEffectSet, SnpChipEffectSet
public static class ChipEffectSet
extends ParameterCelSet
This class represents estimates of chip effects in the probe-level models.
ChipEffectSet(..., probeModel=c("pm"))
ChipEffectSet(..., probeModel=c("pm"))
... |
Arguments passed to |
probeModel |
The specific type of model, e.g. |
Methods:
boxplotStats |
- | |
extractExpressionSet |
- | |
extractMatrix |
- | |
extractTheta |
- | |
findUnitsTodo |
- | |
getAM |
- | |
getAverageFile |
- | |
getCellIndices |
- | |
plotBoxplot |
- | |
readUnits |
- | |
Methods inherited from ParameterCelSet:
extractDataFrame, extractMatrix
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from AffymetrixCelSet:
append, as, as.AffymetrixCelSet, as.character, averageQuantile, byName, byPath, clone, convertToUnique, doCRMAv1, doCRMAv2, doFIRMA, doGCRMA, doRMA, extractAffyBatch, extractFeatureSet, extractMatrix, extractSnpFeatureSet, findByName, getAverage, getAverageAsinh, getAverageFile, getAverageLog, getCdf, getChipType, getData, getIntensities, getPlatform, getTimestamps, getUnitGroupCellMap, getUnitIntensities, getUnitNamesFile, getUnitTypesFile, isDuplicated, justRMA, justSNPRMA, nbrOfArrays, normalizeQuantile, plotDensity, range, readUnits, setCdf, update2, writeSgr
Methods inherited from AffymetrixFileSet:
as, as.AffymetrixFileSet, byPath, getDefaultFullName
Methods inherited from AromaPlatformInterface:
getAromaPlatform, getAromaUflFile, getAromaUgpFile, getChipType, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith
Methods inherited from AromaMicroarrayDataSet:
as.AromaMicroarrayDataSetList, as.AromaMicroarrayDataSetTuple, getAromaFullNameTranslatorSet, getAverageFile, getChipType, getDefaultFullName, getPlatform, setAttributesBy, setAttributesBySampleAnnotationFile, setAttributesBySampleAnnotationSet, validate
Methods inherited from GenericDataFileSet:
[, [[, anyDuplicated, anyNA, append, appendFiles, appendFullNamesTranslator, appendFullNamesTranslatorByNULL, appendFullNamesTranslatorByTabularTextFile, appendFullNamesTranslatorByTabularTextFileSet, appendFullNamesTranslatorBydata.frame, appendFullNamesTranslatorByfunction, appendFullNamesTranslatorBylist, as.character, as.list, byName, byPath, c, clearCache, clearFullNamesTranslator, clone, copyTo, dsApplyInPairs, duplicated, equals, extract, findByName, findDuplicated, getChecksum, getChecksumFileSet, getChecksumObjects, getDefaultFullName, getFile, getFileClass, getFileSize, getFiles, getFullNames, getNames, getOneFile, getPath, getPathnames, getSubdirs, gunzip, gzip, hasFile, indexOf, is.na, names, nbrOfFiles, rep, resetFullNames, setFullNamesTranslator, sortBy, unique, update2, updateFullName, updateFullNames, validate, getFullNameTranslatorSet, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
An object of this class is typically obtained through the
getChipEffectSet()
method for the ProbeLevelModel
class.
Package: aroma.affymetrix
Class ChipEffectTransform
Object
~~|
~~+--
ParametersInterface
~~~~~~~|
~~~~~~~+--
AromaTransform
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
Transform
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
ChipEffectTransform
Directly known subclasses:
AdditiveCovariatesNormalization, ChipEffectGroupMerge, FragmentEquivalentClassNormalization, FragmentLengthNormalization, GcContentNormalization, GcContentNormalization2, SnpChipEffectGroupMerge
public abstract static class ChipEffectTransform
extends Transform
This abstract class represents a transform that transforms chip-effect estimates obtained from probe-level modeling.
ChipEffectTransform(dataSet=NULL, ...)
ChipEffectTransform(dataSet=NULL, ...)
dataSet |
The input data set as an |
... |
Arguments passed to the constructor of |
Subclasses must implement the process()
method.
Methods:
No methods defined.
Methods inherited from Transform:
getOutputDataSet, getOutputFiles
Methods inherited from AromaTransform:
as.character, findFilesTodo, getAsteriskTags, getExpectedOutputFiles, getExpectedOutputFullnames, getFullName, getInputDataSet, getName, getOutputDataSet, getOutputDataSet0, getOutputFiles, getPath, getRootPath, getTags, isDone, process, setTags
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.affymetrix
Class CnagCfhFile
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
CacheKeyInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
AromaMicroarrayDataFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
CnagCfhFile
Directly known subclasses:
public abstract static class CnagCfhFile
extends AffymetrixFile
A CnagCfhFile object represents a single CNAG CFH file.
CnagCfhFile(..., cdf=NULL)
CnagCfhFile(..., cdf=NULL)
... |
Arguments passed to |
cdf |
An optional |
Methods:
getCdf |
- | |
nbrOfCells |
- | |
nbrOfSnps |
- | |
setCdf |
- | |
Methods inherited from AromaPlatformInterface:
getAromaPlatform, getAromaUflFile, getAromaUgpFile, getChipType, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith
Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags
Methods inherited from FileCacheKeyInterface:
getCacheKey
Methods inherited from CacheKeyInterface:
getCacheKey
Methods inherited from GenericDataFile:
as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
An object of this class is typically part of an CnagCfhSet
.
Package: aroma.affymetrix
Class CnagCfhSet
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFileSet
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
CnagCfhSet
Directly known subclasses:
public static class CnagCfhSet
extends GenericDataFileSet
An CnagCfhSet object represents a set of CNAG CFH files with identical chip types.
CnagCfhSet(files=NULL, ...)
CnagCfhSet(files=NULL, ...)
files |
A |
... |
Not used. |
Methods:
as |
- | |
as.CnagCfhSet |
- | |
byName |
- | |
getAverage |
- | |
getAverageAsinh |
- | |
getAverageFile |
- | |
getAverageLog |
- | |
getCdf |
- | |
getData |
- | |
getTimestamps |
- | |
readUnits |
- | |
setCdf |
- | |
Methods inherited from GenericDataFileSet:
[, [[, anyDuplicated, anyNA, append, appendFiles, appendFullNamesTranslator, appendFullNamesTranslatorByNULL, appendFullNamesTranslatorByTabularTextFile, appendFullNamesTranslatorByTabularTextFileSet, appendFullNamesTranslatorBydata.frame, appendFullNamesTranslatorByfunction, appendFullNamesTranslatorBylist, as.character, as.list, byName, byPath, c, clearCache, clearFullNamesTranslator, clone, copyTo, dsApplyInPairs, duplicated, equals, extract, findByName, findDuplicated, getChecksum, getChecksumFileSet, getChecksumObjects, getDefaultFullName, getFile, getFileClass, getFileSize, getFiles, getFullNames, getNames, getOneFile, getPath, getPathnames, getSubdirs, gunzip, gzip, hasFile, indexOf, is.na, names, nbrOfFiles, rep, resetFullNames, setFullNamesTranslator, sortBy, unique, update2, updateFullName, updateFullNames, validate, getFullNameTranslatorSet, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.affymetrix
Class CnChipEffectFile
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
CacheKeyInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
AromaMicroarrayDataFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixCelFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
ParametersInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
ParameterCelFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
ChipEffectFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
SnpChipEffectFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
CopyNumberDataFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
CnChipEffectFile
Directly known subclasses:
public abstract static class CnChipEffectFile
extends CopyNumberDataFile
This class represents estimates of chip effects in a copy-number probe-level models.
CnChipEffectFile(..., combineAlleles=FALSE)
CnChipEffectFile(..., combineAlleles=FALSE)
... |
Arguments passed to |
combineAlleles |
A |
Methods:
exportTotalAndFracB |
- | |
extractTheta |
- | |
extractTotalAndFreqB |
- | |
hasAlleleBFractions |
- | |
hasStrandiness |
- | |
mergeStrands |
- | |
readUnits |
- | |
Methods inherited from CopyNumberDataFile:
as, as.CopyNumberDataFile, getNumberOfFilesAveraged, hasAlleleBFractions, hasStrandiness
Methods inherited from SnpChipEffectFile:
exportTotalAndFracB, extractCNT, extractTheta, extractTotalAndFracB, getCellIndices, getExpandedCellMap, getParameters, mergeStrands, readUnits, writeCNT
Methods inherited from ChipEffectFile:
as.character, extractChromosomalDataFrame, extractMatrix, extractTheta, findUnitsTodo, getAM, getAsFullCelFile, getCellIndices, getCellMapForMainCdf, getExpandedCellMap, getParameters, getUnitGroupCellArrayMap, getUnitGroupCellMatrixMap, getXAM, mergeGroups, readUnits, writeAsFullCelFile
Methods inherited from ParameterCelFile:
extractDataFrame, extractMatrix, readUnits
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from AffymetrixCelFile:
allocateFromCdf, as.character, clone, createFrom, extractMatrix, fromFile, getAm, getCdf, getExtensionPattern, getFileFormat, getImage, getUnitNamesFile, getUnitTypesFile, highlight, image270, nbrOfCells, plotDensity, plotImage, plotMvsA, plotMvsX, range, setCdf, smoothScatterMvsA, writeImage
Methods inherited from AromaPlatformInterface:
getAromaPlatform, getAromaUflFile, getAromaUgpFile, getChipType, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith
Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags
Methods inherited from FileCacheKeyInterface:
getCacheKey
Methods inherited from CacheKeyInterface:
getCacheKey
Methods inherited from GenericDataFile:
as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
An object of this class is typically part of a CnChipEffectSet
.
Package: aroma.affymetrix
Class CnChipEffectSet
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFileSet
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
AromaMicroarrayDataSet
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixFileSet
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixCelSet
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
ParametersInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
ParameterCelSet
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
ChipEffectSet
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
SnpChipEffectSet
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
CopyNumberDataSet
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
CnChipEffectSet
Directly known subclasses:
public static class CnChipEffectSet
extends CopyNumberDataSet
This class represents estimates of chip effects in the probe-level models.
CnChipEffectSet(..., combineAlleles="byFirstFile")
CnChipEffectSet(..., combineAlleles="byFirstFile")
... |
Arguments passed to |
combineAlleles |
A |
Methods:
as.CopyNumberDataSetTuple |
- | |
exportTotalAndFracB |
- | |
extractTheta |
- | |
extractTotalAndFreqB |
- | |
getAverageFile |
- | |
getCombineAlleles |
- | |
hasAlleleBFractions |
- | |
hasStrandiness |
- | |
setCombineAlleles |
- | |
writeWig |
- | |
Methods inherited from CopyNumberDataSet:
as, as.CopyNumberDataSet, doCBS, hasAlleleBFractions, hasStrandiness
Methods inherited from SnpChipEffectSet:
byPath, exportTotalAndFracB, extractAlleleSet, extractCNT, extractSnpCnvQSet, extractSnpQSet, extractTheta, extractTotalAndFreqB, getAverageFile, getBaseline, getMergeStrands, setMergeStrands, writeCNT
Methods inherited from ChipEffectSet:
as.character, boxplotStats, byPath, calculateBaseline, calculateFieldBoxplotStats, calculateNuseBoxplotStats, calculateRleBoxplotStats, extractAffyBatch, extractChromosomalDataFrame, extractExpressionSet, extractMatrix, extractTheta, findByName, findUnitsTodo, fromDataSet, getAM, getAsFullCelSet, getAverageFile, getBaseline, getCellIndices, getXAM, plotBoxplot, readUnits, updateUnits
Methods inherited from ParameterCelSet:
extractDataFrame, extractMatrix
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from AffymetrixCelSet:
append, as, as.AffymetrixCelSet, as.character, averageQuantile, byName, byPath, clone, convertToUnique, doCRMAv1, doCRMAv2, doFIRMA, doGCRMA, doRMA, extractAffyBatch, extractFeatureSet, extractMatrix, extractSnpFeatureSet, findByName, getAverage, getAverageAsinh, getAverageFile, getAverageLog, getCdf, getChipType, getData, getIntensities, getPlatform, getTimestamps, getUnitGroupCellMap, getUnitIntensities, getUnitNamesFile, getUnitTypesFile, isDuplicated, justRMA, justSNPRMA, nbrOfArrays, normalizeQuantile, plotDensity, range, readUnits, setCdf, update2, writeSgr
Methods inherited from AffymetrixFileSet:
as, as.AffymetrixFileSet, byPath, getDefaultFullName
Methods inherited from AromaPlatformInterface:
getAromaPlatform, getAromaUflFile, getAromaUgpFile, getChipType, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith
Methods inherited from AromaMicroarrayDataSet:
as.AromaMicroarrayDataSetList, as.AromaMicroarrayDataSetTuple, getAromaFullNameTranslatorSet, getAverageFile, getChipType, getDefaultFullName, getPlatform, setAttributesBy, setAttributesBySampleAnnotationFile, setAttributesBySampleAnnotationSet, validate
Methods inherited from GenericDataFileSet:
[, [[, anyDuplicated, anyNA, append, appendFiles, appendFullNamesTranslator, appendFullNamesTranslatorByNULL, appendFullNamesTranslatorByTabularTextFile, appendFullNamesTranslatorByTabularTextFileSet, appendFullNamesTranslatorBydata.frame, appendFullNamesTranslatorByfunction, appendFullNamesTranslatorBylist, as.character, as.list, byName, byPath, c, clearCache, clearFullNamesTranslator, clone, copyTo, dsApplyInPairs, duplicated, equals, extract, findByName, findDuplicated, getChecksum, getChecksumFileSet, getChecksumObjects, getDefaultFullName, getFile, getFileClass, getFileSize, getFiles, getFullNames, getNames, getOneFile, getPath, getPathnames, getSubdirs, gunzip, gzip, hasFile, indexOf, is.na, names, nbrOfFiles, rep, resetFullNames, setFullNamesTranslator, sortBy, unique, update2, updateFullName, updateFullNames, validate, getFullNameTranslatorSet, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.affymetrix
Class CnPlm
Interface
~~|
~~+--
SnpPlm
~~~~~~~|
~~~~~~~+--
CnPlm
Directly known subclasses:
AffineCnPlm, AvgCnPlm, HetLogAddCnPlm, MbeiCnPlm, RmaCnPlm
public class CnPlm
extends SnpPlm
This support class represents a SnpPlm
specially designed for
copy-number analysis.
CnPlm(...)
CnPlm(...)
... |
Arguments passed to |
Models implementing this copy-number PLM, provides either
allele-specific or total copy-number estimates.
For allele-specific CNs the underlying SnpPlm
model is fitted as
is, i.e. for each allele separately with or without the strands first
being merged.
For total CNs the probe signals for the two alleles are combined
(=summed; not averaged) on the intensity scale before fitting
underlying SnpPlm
model, again with or without the strands
first being merged.
Methods:
getCellIndices |
- | |
getChipEffectSet |
- | |
getCombineAlleles |
- | |
getProbeAffinityFile |
- | |
setCombineAlleles |
- | |
Methods inherited from SnpPlm:
getCellIndices, getChipEffectSet, getMergeStrands, getParameters, getProbeAffinityFile, setMergeStrands
Methods inherited from Interface:
extend, print, uses
Classes inheriting from this Interface
must provide the
following fields, in addition to the ones according to SnpPlm
:
A logical
indicating if total or allele-specific
copy numbers should be estimated according to the above averaging.
Henrik Bengtsson
Package: aroma.affymetrix
Class CnProbeAffinityFile
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
CacheKeyInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
AromaMicroarrayDataFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixCelFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
ParametersInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
ParameterCelFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
ProbeAffinityFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
SnpProbeAffinityFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
CnProbeAffinityFile
Directly known subclasses:
public abstract static class CnProbeAffinityFile
extends SnpProbeAffinityFile
This class represents estimates of probe affinities in SNP probe-level models.
CnProbeAffinityFile(..., combineAlleles=FALSE)
CnProbeAffinityFile(..., combineAlleles=FALSE)
... |
Arguments passed to |
combineAlleles |
If |
Methods:
No methods defined.
Methods inherited from SnpProbeAffinityFile:
getCellIndices, setMergeStrands
Methods inherited from ProbeAffinityFile:
as.character, getCellIndices, getParameters, readUnits
Methods inherited from ParameterCelFile:
extractDataFrame, extractMatrix, readUnits
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from AffymetrixCelFile:
allocateFromCdf, as.character, clone, createFrom, extractMatrix, fromFile, getAm, getCdf, getExtensionPattern, getFileFormat, getImage, getUnitNamesFile, getUnitTypesFile, highlight, image270, nbrOfCells, plotDensity, plotImage, plotMvsA, plotMvsX, range, setCdf, smoothScatterMvsA, writeImage
Methods inherited from AromaPlatformInterface:
getAromaPlatform, getAromaUflFile, getAromaUgpFile, getChipType, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith
Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags
Methods inherited from FileCacheKeyInterface:
getCacheKey
Methods inherited from CacheKeyInterface:
getCacheKey
Methods inherited from GenericDataFile:
as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.affymetrix
Class CrlmmParametersFile
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
ColumnNamesInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
GenericTabularFile
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
CacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaTabularBinaryFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaUnitSignalBinaryFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
CrlmmParametersFile
Directly known subclasses:
public static class CrlmmParametersFile
extends AromaUnitSignalBinaryFile
An CrlmmParametersFile is a AromaUnitSignalBinaryFile
.
CrlmmParametersFile(...)
CrlmmParametersFile(...)
... |
Arguments passed to |
Methods:
allocate |
- | |
findUnitsTodo |
- | |
readParameter |
- | |
updateParameter |
- | |
Methods inherited from AromaUnitSignalBinaryFile:
allocate, allocateFromUnitAnnotationDataFile, allocateFromUnitNamesFile, as.character, extractMatrix, extractRawGenomicSignals, fromFile, getChipType, getExtensionPattern, getFilenameExtension, getNumberOfFilesAveraged, getPlatform, isAverageFile, nbrOfUnits, readDataFrame, writeDataFrame
Methods inherited from AromaPlatformInterface:
getAromaPlatform, getAromaUflFile, getAromaUgpFile, getChipType, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith
Methods inherited from AromaTabularBinaryFile:
[, [<-, [[, allocate, as.character, colApply, colMeans, colStats, colSums, dimnames<-, getBytesPerColumn, getColClasses, getDefaultColumnNames, getRootName, importFrom, nbrOfColumns, nbrOfRows, readColumns, readDataFrame, readFooter, readHeader, readRawFooter, setAttributesByTags, subset, summary, updateData, updateDataColumn, writeFooter, writeRawFooter
Methods inherited from FileCacheKeyInterface:
getCacheKey
Methods inherited from CacheKeyInterface:
getCacheKey
Methods inherited from GenericTabularFile:
[, as.character, dim, extractMatrix, head, nbrOfColumns, nbrOfRows, readColumns, readDataFrame, tail, writeColumnsToFiles
Methods inherited from ColumnNamesInterface:
appendColumnNamesTranslator, appendColumnNamesTranslatorByNULL, appendColumnNamesTranslatorBycharacter, appendColumnNamesTranslatorByfunction, appendColumnNamesTranslatorBylist, clearColumnNamesTranslator, clearListOfColumnNamesTranslators, getColumnNames, getColumnNamesTranslator, getDefaultColumnNames, getListOfColumnNamesTranslators, nbrOfColumns, setColumnNames, setColumnNamesTranslator, setListOfColumnNamesTranslators, updateColumnNames
Methods inherited from GenericDataFile:
as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.affymetrix
Class CrlmmParametersSet
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFileSet
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
GenericTabularFileSet
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
AromaTabularBinarySet
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
AromaUnitSignalBinarySet
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
CrlmmParametersSet
Directly known subclasses:
public static class CrlmmParametersSet
extends AromaUnitSignalBinarySet
An CrlmmParametersSet object represents a set of
CrlmmParametersFile
s with identical chip types.
CrlmmParametersSet(...)
CrlmmParametersSet(...)
... |
Arguments passed to
|
Methods:
byName |
- | |
byPath |
- | |
findUnitsTodo |
- | |
Methods inherited from AromaUnitSignalBinarySet:
byName, findByName, getAromaFullNameTranslatorSet, getAromaUgpFile, getChipType, getPlatform, validate, writeDataFrame
Methods inherited from AromaTabularBinarySet:
getDefaultFullName, getRootName, setAttributesBy, setAttributesBySampleAnnotationFile, setAttributesBySampleAnnotationSet, setAttributesByTags
Methods inherited from GenericTabularFileSet:
extractMatrix, calculateAverageColumnAcrossFiles
Methods inherited from GenericDataFileSet:
[, [[, anyDuplicated, anyNA, append, appendFiles, appendFullNamesTranslator, appendFullNamesTranslatorByNULL, appendFullNamesTranslatorByTabularTextFile, appendFullNamesTranslatorByTabularTextFileSet, appendFullNamesTranslatorBydata.frame, appendFullNamesTranslatorByfunction, appendFullNamesTranslatorBylist, as.character, as.list, byName, byPath, c, clearCache, clearFullNamesTranslator, clone, copyTo, dsApplyInPairs, duplicated, equals, extract, findByName, findDuplicated, getChecksum, getChecksumFileSet, getChecksumObjects, getDefaultFullName, getFile, getFileClass, getFileSize, getFiles, getFullNames, getNames, getOneFile, getPath, getPathnames, getSubdirs, gunzip, gzip, hasFile, indexOf, is.na, names, nbrOfFiles, rep, resetFullNames, setFullNamesTranslator, sortBy, unique, update2, updateFullName, updateFullNames, validate, getFullNameTranslatorSet, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.affymetrix
Class DChipCdfBinFile
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
CacheKeyInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
AromaMicroarrayDataFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
UnitAnnotationDataFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
UnitNamesFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
DChipCdfBinFile
Directly known subclasses:
public abstract static class DChipCdfBinFile
extends UnitNamesFile
A DChipCdfBinFile object represents a DChip CDF.bin file.
DChipCdfBinFile(...)
DChipCdfBinFile(...)
... |
Arguments passed to |
Methods:
byChipType |
- | |
getChipType |
- | |
getFileFormat |
- | |
getHeader |
- | |
getPlatform |
- | |
getUnitNames |
- | |
getUnitSizes |
- | |
nbrOfCells |
- | |
nbrOfUnits |
- | |
readDataFrame |
- | |
Methods inherited from UnitNamesFile:
getUnitNames, indexOf, nbrOfUnits
Methods inherited from UnitAnnotationDataFile:
byChipType, getAromaUflFile, getAromaUgpFile, getChipType, getDefaultExtension, getPlatform, nbrOfUnits
Methods inherited from AromaPlatformInterface:
getAromaPlatform, getAromaUflFile, getAromaUgpFile, getChipType, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith
Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags
Methods inherited from FileCacheKeyInterface:
getCacheKey
Methods inherited from CacheKeyInterface:
getCacheKey
Methods inherited from GenericDataFile:
as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.affymetrix
Class DChipDcpFile
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
CacheKeyInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
AromaMicroarrayDataFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
DChipDcpFile
Directly known subclasses:
public abstract static class DChipDcpFile
extends AffymetrixFile
A DChipDcpFile object represents a DChip DCP file.
DChipDcpFile(...)
DChipDcpFile(...)
... |
Arguments passed to |
Methods:
dim |
- | |
extractTheta |
- | |
getCalls |
- | |
getExcludes |
- | |
getFileFormat |
- | |
getHeader |
- | |
getNormalizedIntensities |
- | |
getRawIntensities |
- | |
getThetaStds |
- | |
getThetas |
- | |
getThetasAB |
- | |
hasMbeiData |
- | |
hasNormalizedData |
- | |
nbrOfCells |
- | |
nbrOfUnits |
- | |
Methods inherited from AromaPlatformInterface:
getAromaPlatform, getAromaUflFile, getAromaUgpFile, getChipType, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith
Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags
Methods inherited from FileCacheKeyInterface:
getCacheKey
Methods inherited from CacheKeyInterface:
getCacheKey
Methods inherited from GenericDataFile:
as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.affymetrix
Class DChipDcpSet
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFileSet
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
AromaMicroarrayDataSet
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixFileSet
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
DChipDcpSet
Directly known subclasses:
public abstract static class DChipDcpSet
extends AffymetrixFileSet
A DChipDcpSet object represents a set of DChip DCP files for identical chip types.
DChipDcpSet(files=NULL, ...)
DChipDcpSet(files=NULL, ...)
files |
A |
... |
Not used. |
Methods:
as |
- | |
as.DChipDcpSet |
- | |
byName |
- | |
exportTotalAndFracB |
- | |
extractTheta |
- | |
getCdfBin |
- | |
getChipType |
- | |
Methods inherited from AffymetrixFileSet:
as, as.AffymetrixFileSet, byPath, getDefaultFullName
Methods inherited from AromaPlatformInterface:
getAromaPlatform, getAromaUflFile, getAromaUgpFile, getChipType, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith
Methods inherited from AromaMicroarrayDataSet:
as.AromaMicroarrayDataSetList, as.AromaMicroarrayDataSetTuple, getAromaFullNameTranslatorSet, getAverageFile, getChipType, getDefaultFullName, getPlatform, setAttributesBy, setAttributesBySampleAnnotationFile, setAttributesBySampleAnnotationSet, validate
Methods inherited from GenericDataFileSet:
[, [[, anyDuplicated, anyNA, append, appendFiles, appendFullNamesTranslator, appendFullNamesTranslatorByNULL, appendFullNamesTranslatorByTabularTextFile, appendFullNamesTranslatorByTabularTextFileSet, appendFullNamesTranslatorBydata.frame, appendFullNamesTranslatorByfunction, appendFullNamesTranslatorBylist, as.character, as.list, byName, byPath, c, clearCache, clearFullNamesTranslator, clone, copyTo, dsApplyInPairs, duplicated, equals, extract, findByName, findDuplicated, getChecksum, getChecksumFileSet, getChecksumObjects, getDefaultFullName, getFile, getFileClass, getFileSize, getFiles, getFullNames, getNames, getOneFile, getPath, getPathnames, getSubdirs, gunzip, gzip, hasFile, indexOf, is.na, names, nbrOfFiles, rep, resetFullNames, setFullNamesTranslator, sortBy, unique, update2, updateFullName, updateFullNames, validate, getFullNameTranslatorSet, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.affymetrix
Class DChipGenomeInformation
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
CacheKeyInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
GenomeInformation
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
DChipGenomeInformation
Directly known subclasses:
public abstract static class DChipGenomeInformation
extends GenomeInformation
This class represents dChip genome information files, which typically contains information about chromosomal locations of the units.
DChipGenomeInformation(...)
DChipGenomeInformation(...)
... |
Arguments passed to |
The dChip genome information files for various chip types can be
downloaded from https://sites.google.com/site/dchipsoft/.
Put each file in a
directory named identically as the corresponding chip type under the
annotations/ directory, e.g.
annotations/Mapping50K_Hind240/50k hind genome info AfAm
june 05 hg17.xls.
Note that dChip changes the filename and file format slightly between
chip types, but currently the *byChipType()
basically searches
for files with names consisting of "genome info"
or
"genome_info"
. At least for the most common chip types, there
is no need to rename the files in order for this class to recognize them.
Methods:
byChipType |
- | |
readDataFrame |
- | |
Methods inherited from GenomeInformation:
as.character, byChipType, fromCdf, fromDataSet, getChipType, getChromosomeStats, getChromosomes, getData, getPositions, getUnitIndices, getUnitsOnChromosome, getUnitsOnChromosomes, isCompatibleWithCdf, nbrOfUnits, plotDensity, readDataFrame, verify
Methods inherited from FileCacheKeyInterface:
getCacheKey
Methods inherited from CacheKeyInterface:
getCacheKey
Methods inherited from GenericDataFile:
as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.affymetrix
Class DChipQuantileNormalization
Object
~~|
~~+--
ParametersInterface
~~~~~~~|
~~~~~~~+--
AromaTransform
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
Transform
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
ProbeLevelTransform
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
QuantileNormalization
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
DChipQuantileNormalization
Directly known subclasses:
public static class DChipQuantileNormalization
extends QuantileNormalization
This class represents a special QuantileNormalization
using smooth-splines.
DChipQuantileNormalization(..., robust=FALSE)
DChipQuantileNormalization(..., robust=FALSE)
... |
Arguments passed to the constructor of
|
robust |
If |
This normalization method implements the two-pass algorithm described in Bengtsson et al. (2008).
Methods:
process |
- | |
Methods inherited from QuantileNormalization:
findTargetDistributionFile, getParameters, process
Methods inherited from ProbeLevelTransform:
getRootPath
Methods inherited from Transform:
getOutputDataSet, getOutputFiles
Methods inherited from AromaTransform:
as.character, findFilesTodo, getAsteriskTags, getExpectedOutputFiles, getExpectedOutputFullnames, getFullName, getInputDataSet, getName, getOutputDataSet, getOutputDataSet0, getOutputFiles, getPath, getRootPath, getTags, isDone, process, setTags
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
[1] H. Bengtsson, R. Irizarry, B. Carvalho, & T.P. Speed. Estimation and assessment of raw copy numbers at the single locus level, Bioinformatics, 2008.
Package: aroma.affymetrix
Class DChipSnpInformation
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
CacheKeyInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
SnpInformation
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
DChipSnpInformation
Directly known subclasses:
public abstract static class DChipSnpInformation
extends SnpInformation
This class represents dChip genome information files, which typically contains information on nucleotide sequences and fragment lengths of the units.
DChipSnpInformation(...)
DChipSnpInformation(...)
... |
Arguments passed to |
The dChip SNP information files for various chip types can be
downloaded from https://sites.google.com/site/dchipsoft/.
Put each file in a
directory named identically as the corresponding chip type under the
annotations/ directory, e.g.
annotations/Mapping50K_Hind240/50k hind snp info AfAm
june 05 hg17.xls.
Note that dChip changes the filename and file format slightly between
chip types, but currently the *byChipType()
basically searches
for files with names consisting of "snp info"
or
"snp_info"
. At least for the most common chip types, there
is no need to rename the files in order for this class to recognize them.
Methods:
byChipType |
- | |
readDataFrame |
- | |
Methods inherited from SnpInformation:
as.character, byChipType, fromCdf, fromDataSet, getChipType, getData, getFields, getFragmentLengths, getFragmentStarts, getFragmentStops, isCompatibleWithCdf, nbrOfEnzymes, nbrOfUnits, readDataFrame, verify
Methods inherited from FileCacheKeyInterface:
getCacheKey
Methods inherited from CacheKeyInterface:
getCacheKey
Methods inherited from GenericDataFile:
as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Estimation and assessment of raw copy numbers at the single locus level (CRMA v1) based on [1]. The algorithm is processed in bounded memory, meaning virtually any number of arrays can be analyzed on also very limited computer systems.
## S3 method for class 'AffymetrixCelSet' doCRMAv1(csR, shift=+300, combineAlleles=TRUE, lengthRange=NULL, arrays=NULL, drop=TRUE, verbose=FALSE, ...) ## Default S3 method: doCRMAv1(dataSet, ..., verbose=FALSE) ## Default S3 method: doASCRMAv1(...)
## S3 method for class 'AffymetrixCelSet' doCRMAv1(csR, shift=+300, combineAlleles=TRUE, lengthRange=NULL, arrays=NULL, drop=TRUE, verbose=FALSE, ...) ## Default S3 method: doCRMAv1(dataSet, ..., verbose=FALSE) ## Default S3 method: doASCRMAv1(...)
csR , dataSet
|
An |
shift |
An tuning parameter specifying how much to shift the probe signals before probe summarization. |
combineAlleles |
A |
lengthRange |
An optional |
arrays |
A |
drop |
If |
verbose |
See |
... |
Additional arguments used to set up |
Returns a named list
, iff drop == FALSE
, otherwise
only ChipEffectSet
object.
If you wish to obtain allele-specific estimates for SNPs, which
are needed to call genotypes or infer parent-specific copy numbers,
then use argument combineAlleles=FALSE
. Total copy number
signals are still available.
If you know for certain that you will not use allele-specific
estimates, you will get slightly less noisy signals
(very small difference) if you use combineAlleles=TRUE
.
doASCRMAv1(...)
is a wrapper for
doCRMAv1(..., combineAlleles=FALSE)
.
Henrik Bengtsson
[1] H. Bengtsson, R. Irizarry, B. Carvalho & T.P. Speed.
Estimation and assessment of raw copy numbers at the
single locus level,
Bioinformatics, 2008.
For CRMA v2 (recommended by authors), which is a single-array
improvement over CRMA v1, see doCRMAv2
().
A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays (CRMA v2) based on [1]. The algorithm is processed in bounded memory, meaning virtually any number of arrays can be analyzed on also very limited computer systems.
We recommend CRMA v2 for estimating allele-specific as well total SNP signals from Affymetrix SNP chips.
## S3 method for class 'AffymetrixCelSet' doCRMAv2(csR, combineAlleles=TRUE, lengthRange=NULL, arrays=NULL, plm=c("AvgCnPlm", "RmaCnPlm"), drop=TRUE, verbose=FALSE, ...) ## Default S3 method: doCRMAv2(dataSet, ..., verbose=FALSE) ## Default S3 method: doASCRMAv2(...)
## S3 method for class 'AffymetrixCelSet' doCRMAv2(csR, combineAlleles=TRUE, lengthRange=NULL, arrays=NULL, plm=c("AvgCnPlm", "RmaCnPlm"), drop=TRUE, verbose=FALSE, ...) ## Default S3 method: doCRMAv2(dataSet, ..., verbose=FALSE) ## Default S3 method: doASCRMAv2(...)
csR , dataSet
|
An |
combineAlleles |
A |
lengthRange |
An optional |
arrays |
A |
plm |
A |
drop |
If |
verbose |
See |
... |
Additional arguments used to set up |
Returns a named list
, iff drop == FALSE
, otherwise
only ChipEffectSet
object.
If you wish to obtain allele-specific estimates for SNPs, which
are needed to call genotypes or infer parent-specific copy numbers,
then use argument combineAlleles=FALSE
. Total copy number
signals are still available.
If you know for certain that you will not use allele-specific
estimates, you will get slightly less noisy signals
(very small difference) if you use combineAlleles=TRUE
.
doASCRMAv2(...)
is a wrapper for
doCRMAv2(..., combineAlleles=FALSE)
.
Henrik Bengtsson
[1] H. Bengtsson, P. Wirapati & T.P. Speed.
A single-array preprocessing method for estimating
full-resolution raw copy numbers from all Affymetrix
genotyping arrays including GenomeWideSNP 5 & 6,
Bioinformatics, 2009.
For CRMA v1, which is a multi-array methods that precedes CRMA v2,
see doCRMAv1
().
Finding Isoforms using Robust Multichip Analysis (FIRMA) based on [1].
## S3 method for class 'AffymetrixCelSet' doFIRMA(csR, ..., flavor=c("v1b", "v1a"), drop=TRUE, verbose=FALSE) ## Default S3 method: doFIRMA(dataSet, ..., verbose=FALSE)
## S3 method for class 'AffymetrixCelSet' doFIRMA(csR, ..., flavor=c("v1b", "v1a"), drop=TRUE, verbose=FALSE) ## Default S3 method: doFIRMA(dataSet, ..., verbose=FALSE)
csR , dataSet
|
An |
... |
Additional arguments passed to |
flavor |
A |
drop |
If |
verbose |
See |
Returns a named list
, iff drop == FALSE
, otherwise
only FirmaSet
object (containing the FIRMA scores).
It is strongly recommended to use a custom CDF, e.g. "core",
"extended" or "full" [1]. To use a custom CDF, set it before
calling this method, i.e. setCdf(csR, cdf)
.
Do not set the standard "non-supported" Affymetrix CDF
(see also Section 'Flavors').
If flavor == "v1b"
(default), then the standard
"non-supported" Affymetrix CDF is used for background correction
and the quantile normalization steps, and the custom CDF
is used for the probe summarization and everything that follows.
The advantage of this flavor is that those two first preprocessing
steps will remain the same if one later changes to a different
custom CDF.
If flavor == "v1a"
, then the custom CDF is used throughout
all steps of FIRMA, which means that if one changes the custom CDF
all steps will be redone.
Henrik Bengtsson
[1] E. Purdom, K. Simpson, M. Robinson, J. Conboy, A. Lapuk & T.P. Speed,
FIRMA: a method for detection of alternative splicing from
exon array data, Bioinformatics, 2008.
Robust Multichip Analysis (GCRMA) based on [1].
The algorithm is processed in bounded memory, meaning virtually
any number of arrays can be analyzed on also very limited computer
systems.
The method replicates the results of gcrma
(package gcrma) with great precision.
## S3 method for class 'AffymetrixCelSet' doGCRMA(csR, arrays=NULL, type=c("fullmodel", "affinities"), uniquePlm=FALSE, drop=TRUE, verbose=FALSE, ...) ## Default S3 method: doGCRMA(dataSet, ..., verbose=FALSE)
## S3 method for class 'AffymetrixCelSet' doGCRMA(csR, arrays=NULL, type=c("fullmodel", "affinities"), uniquePlm=FALSE, drop=TRUE, verbose=FALSE, ...) ## Default S3 method: doGCRMA(dataSet, ..., verbose=FALSE)
csR , dataSet
|
An |
arrays |
A |
type |
A |
uniquePlm |
If |
drop |
If |
verbose |
See |
... |
Additional arguments used to set up |
Returns a named list
, iff drop == FALSE
, otherwise
only ChipEffectSet
object.
Henrik Bengtsson
[1] Z. Wu, R. Irizarry, R. Gentleman, F.M. Murillo & F. Spencer.
A Model Based Background Adjustment for Oligonucleotide
Expression Arrays, JASA, 2004.
Robust Multichip Analysis (RMA) based on [1].
The algorithm is processed in bounded memory, meaning virtually
any number of arrays can be analyzed on also very limited computer
systems.
The method replicates the results of fitPLM
(package affyPLM) with great precision.
## S3 method for class 'AffymetrixCelSet' doRMA(csR, arrays=NULL, flavor=c("affyPLM", "oligo"), uniquePlm=FALSE, drop=TRUE, verbose=FALSE, ...) ## Default S3 method: doRMA(dataSet, ..., verbose=FALSE)
## S3 method for class 'AffymetrixCelSet' doRMA(csR, arrays=NULL, flavor=c("affyPLM", "oligo"), uniquePlm=FALSE, drop=TRUE, verbose=FALSE, ...) ## Default S3 method: doRMA(dataSet, ..., verbose=FALSE)
csR , dataSet
|
An |
arrays |
A |
flavor |
A character string specifying what model fitting algorithm to be used, cf. |
uniquePlm |
If |
drop |
If |
verbose |
See |
... |
Additional arguments used to set up |
Returns a named list
, iff drop == FALSE
, otherwise
only ChipEffectSet
object.
Henrik Bengtsson
[1] Irizarry et al.
Summaries of Affymetrix GeneChip probe level data.
NAR, 2003, 31, e15.
Package: aroma.affymetrix
Class ExonChipEffectFile
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
CacheKeyInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
AromaMicroarrayDataFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixCelFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
ParametersInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
ParameterCelFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
ChipEffectFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
ExonChipEffectFile
Directly known subclasses:
public abstract static class ExonChipEffectFile
extends ChipEffectFile
This class represents estimates of chip effects in the probe-level models.
ExonChipEffectFile(..., mergeGroups=FALSE)
ExonChipEffectFile(..., mergeGroups=FALSE)
... |
Arguments passed to |
mergeGroups |
Specifies if the groups are merged or not for these estimates. |
Methods:
readUnits |
- | |
Methods inherited from ChipEffectFile:
as.character, extractChromosomalDataFrame, extractMatrix, extractTheta, findUnitsTodo, getAM, getAsFullCelFile, getCellIndices, getCellMapForMainCdf, getExpandedCellMap, getParameters, getUnitGroupCellArrayMap, getUnitGroupCellMatrixMap, getXAM, mergeGroups, readUnits, writeAsFullCelFile
Methods inherited from ParameterCelFile:
extractDataFrame, extractMatrix, readUnits
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from AffymetrixCelFile:
allocateFromCdf, as.character, clone, createFrom, extractMatrix, fromFile, getAm, getCdf, getExtensionPattern, getFileFormat, getImage, getUnitNamesFile, getUnitTypesFile, highlight, image270, nbrOfCells, plotDensity, plotImage, plotMvsA, plotMvsX, range, setCdf, smoothScatterMvsA, writeImage
Methods inherited from AromaPlatformInterface:
getAromaPlatform, getAromaUflFile, getAromaUgpFile, getChipType, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith
Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags
Methods inherited from FileCacheKeyInterface:
getCacheKey
Methods inherited from CacheKeyInterface:
getCacheKey
Methods inherited from GenericDataFile:
as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Ken Simpson, Henrik Bengtsson
An object of this class is typically part of a ExonChipEffectSet
.
Package: aroma.affymetrix
Class ExonChipEffectSet
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFileSet
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
AromaMicroarrayDataSet
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixFileSet
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixCelSet
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
ParametersInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
ParameterCelSet
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
ChipEffectSet
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
ExonChipEffectSet
Directly known subclasses:
public static class ExonChipEffectSet
extends ChipEffectSet
This class represents estimates of chip effects in the probe-level models.
ExonChipEffectSet(..., mergeGroups=TRUE)
ExonChipEffectSet(..., mergeGroups=TRUE)
... |
Arguments passed to |
mergeGroups |
Specifies if groups (individual exons in a CDF file) are merged or not for these estimates, i.e. whether transcript-level expression is to be estimated. |
Methods:
findUnitsTodo |
- | |
getAverageFile |
- | |
getMergeGroups |
- | |
setMergeGroups |
- | |
Methods inherited from ChipEffectSet:
as.character, boxplotStats, byPath, calculateBaseline, calculateFieldBoxplotStats, calculateNuseBoxplotStats, calculateRleBoxplotStats, extractAffyBatch, extractChromosomalDataFrame, extractExpressionSet, extractMatrix, extractTheta, findByName, findUnitsTodo, fromDataSet, getAM, getAsFullCelSet, getAverageFile, getBaseline, getCellIndices, getXAM, plotBoxplot, readUnits, updateUnits
Methods inherited from ParameterCelSet:
extractDataFrame, extractMatrix
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from AffymetrixCelSet:
append, as, as.AffymetrixCelSet, as.character, averageQuantile, byName, byPath, clone, convertToUnique, doCRMAv1, doCRMAv2, doFIRMA, doGCRMA, doRMA, extractAffyBatch, extractFeatureSet, extractMatrix, extractSnpFeatureSet, findByName, getAverage, getAverageAsinh, getAverageFile, getAverageLog, getCdf, getChipType, getData, getIntensities, getPlatform, getTimestamps, getUnitGroupCellMap, getUnitIntensities, getUnitNamesFile, getUnitTypesFile, isDuplicated, justRMA, justSNPRMA, nbrOfArrays, normalizeQuantile, plotDensity, range, readUnits, setCdf, update2, writeSgr
Methods inherited from AffymetrixFileSet:
as, as.AffymetrixFileSet, byPath, getDefaultFullName
Methods inherited from AromaPlatformInterface:
getAromaPlatform, getAromaUflFile, getAromaUgpFile, getChipType, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith
Methods inherited from AromaMicroarrayDataSet:
as.AromaMicroarrayDataSetList, as.AromaMicroarrayDataSetTuple, getAromaFullNameTranslatorSet, getAverageFile, getChipType, getDefaultFullName, getPlatform, setAttributesBy, setAttributesBySampleAnnotationFile, setAttributesBySampleAnnotationSet, validate
Methods inherited from GenericDataFileSet:
[, [[, anyDuplicated, anyNA, append, appendFiles, appendFullNamesTranslator, appendFullNamesTranslatorByNULL, appendFullNamesTranslatorByTabularTextFile, appendFullNamesTranslatorByTabularTextFileSet, appendFullNamesTranslatorBydata.frame, appendFullNamesTranslatorByfunction, appendFullNamesTranslatorBylist, as.character, as.list, byName, byPath, c, clearCache, clearFullNamesTranslator, clone, copyTo, dsApplyInPairs, duplicated, equals, extract, findByName, findDuplicated, getChecksum, getChecksumFileSet, getChecksumObjects, getDefaultFullName, getFile, getFileClass, getFileSize, getFiles, getFullNames, getNames, getOneFile, getPath, getPathnames, getSubdirs, gunzip, gzip, hasFile, indexOf, is.na, names, nbrOfFiles, rep, resetFullNames, setFullNamesTranslator, sortBy, unique, update2, updateFullName, updateFullNames, validate, getFullNameTranslatorSet, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Ken Simpson, Henrik Bengtsson
Package: aroma.affymetrix
Class ExonProbeAffinityFile
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
CacheKeyInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
AromaMicroarrayDataFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixCelFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
ParametersInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
ParameterCelFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
ProbeAffinityFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
ExonProbeAffinityFile
Directly known subclasses:
public abstract static class ExonProbeAffinityFile
extends ProbeAffinityFile
This class represents estimates of probe affinities in exon array probe-level models.
ExonProbeAffinityFile(..., mergeGroups=FALSE)
ExonProbeAffinityFile(..., mergeGroups=FALSE)
... |
Arguments passed to |
mergeGroups |
Specifies if the groups (exons) are merged or not for these estimates. |
Methods:
No methods defined.
Methods inherited from ProbeAffinityFile:
as.character, getCellIndices, getParameters, readUnits
Methods inherited from ParameterCelFile:
extractDataFrame, extractMatrix, readUnits
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from AffymetrixCelFile:
allocateFromCdf, as.character, clone, createFrom, extractMatrix, fromFile, getAm, getCdf, getExtensionPattern, getFileFormat, getImage, getUnitNamesFile, getUnitTypesFile, highlight, image270, nbrOfCells, plotDensity, plotImage, plotMvsA, plotMvsX, range, setCdf, smoothScatterMvsA, writeImage
Methods inherited from AromaPlatformInterface:
getAromaPlatform, getAromaUflFile, getAromaUgpFile, getChipType, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith
Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags
Methods inherited from FileCacheKeyInterface:
getCacheKey
Methods inherited from CacheKeyInterface:
getCacheKey
Methods inherited from GenericDataFile:
as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Ken Simpson, Henrik Bengtsson
Package: aroma.affymetrix
Class ExonRmaPlm
Object
~~|
~~+--
ParametersInterface
~~~~~~~|
~~~~~~~+--
Model
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
UnitModel
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
MultiArrayUnitModel
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
ProbeLevelModel
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
RmaPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
ExonRmaPlm
Directly known subclasses:
public abstract static class ExonRmaPlm
extends RmaPlm
This class represents the log-additive model part of the Robust Multichip Analysis (RMA) method described in Irizarry et al (2003), as implemented for exon arrays. The model may be fitted with exons merged into transcripts (all probes fitted together) or on an individual exon basis (probes within an exon treated as a group, but exons fitted separately).
ExonRmaPlm(..., mergeGroups=TRUE)
ExonRmaPlm(..., mergeGroups=TRUE)
... |
Arguments passed to |
mergeGroups |
A |
Methods:
getCellIndices |
- | |
getChipEffectSet |
- | |
getProbeAffinityFile |
- | |
setMergeGroups |
- | |
Methods inherited from RmaPlm:
getAsteriskTags, getCalculateResidualsFunction, getParameters, getRlmFitFunctions
Methods inherited from ProbeLevelModel:
calculateResidualSet, calculateWeights, fit, getAsteriskTags, getCalculateResidualsFunction, getChipEffectSet, getProbeAffinityFile, getResidualSet, getRootPath, getWeightsSet
Methods inherited from MultiArrayUnitModel:
getListOfPriors, setListOfPriors, validate
Methods inherited from UnitModel:
findUnitsTodo, getAsteriskTags, getFitSingleCellUnitFunction, getParameters
Methods inherited from Model:
as.character, fit, getAlias, getAsteriskTags, getDataSet, getFullName, getName, getPath, getRootPath, getTags, setAlias, setTags
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Ken Simpson, Henrik Bengtsson, Elizabeth Purdom
Irizarry et al. Summaries of Affymetrix GeneChip probe level data.
NAR, 2003, 31, e15.
Package: aroma.affymetrix
Class FirmaFile
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
CacheKeyInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
AromaMicroarrayDataFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixCelFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
ParametersInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
ParameterCelFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
FirmaFile
Directly known subclasses:
public abstract static class FirmaFile
extends ParameterCelFile
This class represents scores calculated by the FIRMA algorithm.
FirmaFile(...)
FirmaFile(...)
... |
Arguments passed to |
Methods:
extractMatrix |
- | |
findUnitsTodo |
- | |
readUnits |
- | |
Methods inherited from ParameterCelFile:
extractDataFrame, extractMatrix, readUnits
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from AffymetrixCelFile:
allocateFromCdf, as.character, clone, createFrom, extractMatrix, fromFile, getAm, getCdf, getExtensionPattern, getFileFormat, getImage, getUnitNamesFile, getUnitTypesFile, highlight, image270, nbrOfCells, plotDensity, plotImage, plotMvsA, plotMvsX, range, setCdf, smoothScatterMvsA, writeImage
Methods inherited from AromaPlatformInterface:
getAromaPlatform, getAromaUflFile, getAromaUgpFile, getChipType, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith
Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags
Methods inherited from FileCacheKeyInterface:
getCacheKey
Methods inherited from CacheKeyInterface:
getCacheKey
Methods inherited from GenericDataFile:
as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Ken Simpson, Henrik Bengtsson
An object of this class is typically part of a FirmaSet
.
Package: aroma.affymetrix
Class FirmaModel
Object
~~|
~~+--
ParametersInterface
~~~~~~~|
~~~~~~~+--
Model
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
UnitModel
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
FirmaModel
Directly known subclasses:
public abstract static class FirmaModel
extends UnitModel
This class represents the FIRMA (Finding Isoforms using RMA) alternative splicing model.
FirmaModel(rmaPlm=NULL, summaryMethod=c("median", "upperQuartile", "max"), operateOn=c("residuals", "weights"), ...)
FirmaModel(rmaPlm=NULL, summaryMethod=c("median", "upperQuartile", "max"), operateOn=c("residuals", "weights"), ...)
rmaPlm |
An @RmaPlm object. |
summaryMethod |
A |
operateOn |
A |
... |
Arguments passed to constructor of |
Methods:
fit |
- | |
getCdf |
- | |
getDataSet |
- | |
getFirmaSet |
- | |
getName |
- | |
getPlm |
- | |
getTags |
- | |
Methods inherited from UnitModel:
findUnitsTodo, getAsteriskTags, getFitSingleCellUnitFunction, getParameters
Methods inherited from Model:
as.character, fit, getAlias, getAsteriskTags, getDataSet, getFullName, getName, getPath, getRootPath, getTags, setAlias, setTags
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Ken Simpson, Henrik Bengtsson
Package: aroma.affymetrix
Class FirmaSet
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFileSet
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
AromaMicroarrayDataSet
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixFileSet
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixCelSet
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
ParametersInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
ParameterCelSet
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
FirmaSet
Directly known subclasses:
public static class FirmaSet
extends ParameterCelSet
FirmaSet(...)
FirmaSet(...)
... |
Arguments passed to constructor of |
Methods:
extractMatrix |
- | |
findUnitsTodo |
- | |
getCellIndices |
- | |
readUnits |
- | |
Methods inherited from ParameterCelSet:
extractDataFrame, extractMatrix
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from AffymetrixCelSet:
append, as, as.AffymetrixCelSet, as.character, averageQuantile, byName, byPath, clone, convertToUnique, doCRMAv1, doCRMAv2, doFIRMA, doGCRMA, doRMA, extractAffyBatch, extractFeatureSet, extractMatrix, extractSnpFeatureSet, findByName, getAverage, getAverageAsinh, getAverageFile, getAverageLog, getCdf, getChipType, getData, getIntensities, getPlatform, getTimestamps, getUnitGroupCellMap, getUnitIntensities, getUnitNamesFile, getUnitTypesFile, isDuplicated, justRMA, justSNPRMA, nbrOfArrays, normalizeQuantile, plotDensity, range, readUnits, setCdf, update2, writeSgr
Methods inherited from AffymetrixFileSet:
as, as.AffymetrixFileSet, byPath, getDefaultFullName
Methods inherited from AromaPlatformInterface:
getAromaPlatform, getAromaUflFile, getAromaUgpFile, getChipType, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith
Methods inherited from AromaMicroarrayDataSet:
as.AromaMicroarrayDataSetList, as.AromaMicroarrayDataSetTuple, getAromaFullNameTranslatorSet, getAverageFile, getChipType, getDefaultFullName, getPlatform, setAttributesBy, setAttributesBySampleAnnotationFile, setAttributesBySampleAnnotationSet, validate
Methods inherited from GenericDataFileSet:
[, [[, anyDuplicated, anyNA, append, appendFiles, appendFullNamesTranslator, appendFullNamesTranslatorByNULL, appendFullNamesTranslatorByTabularTextFile, appendFullNamesTranslatorByTabularTextFileSet, appendFullNamesTranslatorBydata.frame, appendFullNamesTranslatorByfunction, appendFullNamesTranslatorBylist, as.character, as.list, byName, byPath, c, clearCache, clearFullNamesTranslator, clone, copyTo, dsApplyInPairs, duplicated, equals, extract, findByName, findDuplicated, getChecksum, getChecksumFileSet, getChecksumObjects, getDefaultFullName, getFile, getFileClass, getFileSize, getFiles, getFullNames, getNames, getOneFile, getPath, getPathnames, getSubdirs, gunzip, gzip, hasFile, indexOf, is.na, names, nbrOfFiles, rep, resetFullNames, setFullNamesTranslator, sortBy, unique, update2, updateFullName, updateFullNames, validate, getFullNameTranslatorSet, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Ken Simpson, Henrik Bengtsson
Package: aroma.affymetrix
Class FragmentEquivalentClassNormalization
Object
~~|
~~+--
ParametersInterface
~~~~~~~|
~~~~~~~+--
AromaTransform
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
Transform
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
ChipEffectTransform
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
FragmentEquivalentClassNormalization
Directly known subclasses:
public static class FragmentEquivalentClassNormalization
extends ChipEffectTransform
This class represents a normalization method that corrects for systematic effects between loci of different equivalent classes of pairs of sequences that are recognized by the restriction enzymes that cut the DNA studies.
FragmentEquivalentClassNormalization(dataSet=NULL, ..., targetAvgs=NULL, subsetToFit="-XY")
FragmentEquivalentClassNormalization(dataSet=NULL, ..., targetAvgs=NULL, subsetToFit="-XY")
dataSet |
|
... |
Additional arguments passed to the constructor of
|
targetAvgs |
An optional list of |
subsetToFit |
The units from which the normalization curve should
be estimated. If |
Methods:
getAromaUfcFile |
- | |
getCdf |
- | |
process |
- | |
Methods inherited from ChipEffectTransform:
getRootPath
Methods inherited from Transform:
getOutputDataSet, getOutputFiles
Methods inherited from AromaTransform:
as.character, findFilesTodo, getAsteriskTags, getExpectedOutputFiles, getExpectedOutputFullnames, getFullName, getInputDataSet, getName, getOutputDataSet, getOutputDataSet0, getOutputFiles, getPath, getRootPath, getTags, isDone, process, setTags
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
This class requires an UFC (Unit Fragment Class) annotation file.
The idea of normalization signals stratified on enzyme recognition sequences is credited to Jim Veitch and Ben Bolstad at Affymetrix Inc. (2008) who have designed a similar method for copy number estimation in the Affymetrix' Genotype Console v2.
Henrik Bengtsson
Package: aroma.affymetrix
Class FragmentLengthNormalization
Object
~~|
~~+--
ParametersInterface
~~~~~~~|
~~~~~~~+--
AromaTransform
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
Transform
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
ChipEffectTransform
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
FragmentLengthNormalization
Directly known subclasses:
public static class FragmentLengthNormalization
extends ChipEffectTransform
This class represents a normalization method that corrects for PCR fragment length effects on copy-number chip-effect estimates.
FragmentLengthNormalization(dataSet=NULL, ..., target=targetFunctions, subsetToFit="-XY", lengthRange=NULL, onMissing=c("median", "ignore"), shift=0, targetFunctions=NULL)
FragmentLengthNormalization(dataSet=NULL, ..., target=targetFunctions, subsetToFit="-XY", lengthRange=NULL, onMissing=c("median", "ignore"), shift=0, targetFunctions=NULL)
dataSet |
|
... |
Additional arguments passed to the constructor of
|
target |
(Optional) A |
subsetToFit |
The units from which the normalization curve should
be estimated. If |
lengthRange |
If given, a |
onMissing |
Specifies how to normalize units for which the fragment lengths are unknown. |
shift |
An optional amount the data points should be shifted (translated). |
targetFunctions |
Deprecated. |
For SNPs, the normalization function is estimated based on the total chip effects, i.e. the sum of the allele signals. The normalizing is done by rescale the chip effects on the intensity scale such that the mean of the total chip effects are the same across samples for any given fragment length. For allele-specific estimates, both alleles are always rescaled by the same amount. Thus, when normalizing allele-specific chip effects, the total chip effects is change, but not the relative allele signal, e.g. the allele B frequency.
Methods:
getCdf |
- | |
process |
- | |
Methods inherited from ChipEffectTransform:
getRootPath
Methods inherited from Transform:
getOutputDataSet, getOutputFiles
Methods inherited from AromaTransform:
as.character, findFilesTodo, getAsteriskTags, getExpectedOutputFiles, getExpectedOutputFullnames, getFullName, getInputDataSet, getName, getOutputDataSet, getOutputDataSet0, getOutputFiles, getPath, getRootPath, getTags, isDone, process, setTags
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
This class requires a SNP information annotation file for the chip type to be normalized.
Henrik Bengtsson
Package: aroma.affymetrix
Class GcContentNormalization
Object
~~|
~~+--
ParametersInterface
~~~~~~~|
~~~~~~~+--
AromaTransform
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
Transform
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
ChipEffectTransform
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
GcContentNormalization
Directly known subclasses:
public static class GcContentNormalization
extends ChipEffectTransform
GcContentNormalization(dataSet=NULL, ..., targetFunction=NULL, subsetToFit=NULL)
GcContentNormalization(dataSet=NULL, ..., targetFunction=NULL, subsetToFit=NULL)
dataSet |
|
... |
Additional arguments passed to the constructor of
|
targetFunction |
A |
subsetToFit |
The units from which the normalization curve should
be estimated. If |
Methods:
getCdf |
- | |
process |
- | |
Methods inherited from ChipEffectTransform:
getRootPath
Methods inherited from Transform:
getOutputDataSet, getOutputFiles
Methods inherited from AromaTransform:
as.character, findFilesTodo, getAsteriskTags, getExpectedOutputFiles, getExpectedOutputFullnames, getFullName, getInputDataSet, getName, getOutputDataSet, getOutputDataSet0, getOutputFiles, getPath, getRootPath, getTags, isDone, process, setTags
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
This class requires an Aroma unit GC-content (UGC) file.
Henrik Bengtsson
Package: aroma.affymetrix
Class GcContentNormalization2
Object
~~|
~~+--
ParametersInterface
~~~~~~~|
~~~~~~~+--
AromaTransform
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
Transform
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
ChipEffectTransform
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
AdditiveCovariatesNormalization
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
GcContentNormalization2
Directly known subclasses:
public static class GcContentNormalization2
extends AdditiveCovariatesNormalization
This class represents a normalization method that corrects for annotation-data covariate effects on copy-number chip-effect estimates.
GcContentNormalization2(...)
GcContentNormalization2(...)
... |
Arguments passed to the constructor of
|
Methods:
plotCovariateEffects |
- | |
Methods inherited from AdditiveCovariatesNormalization:
getAsteriskTags, getCdf, getCovariates, getOutputDataSet00, getParameters, process
Methods inherited from ChipEffectTransform:
getRootPath
Methods inherited from Transform:
getOutputDataSet, getOutputFiles
Methods inherited from AromaTransform:
as.character, findFilesTodo, getAsteriskTags, getExpectedOutputFiles, getExpectedOutputFullnames, getFullName, getInputDataSet, getName, getOutputDataSet, getOutputDataSet0, getOutputFiles, getPath, getRootPath, getTags, isDone, process, setTags
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.affymetrix
Class GcRmaBackgroundCorrection
Object
~~|
~~+--
ParametersInterface
~~~~~~~|
~~~~~~~+--
AromaTransform
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
Transform
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
ProbeLevelTransform
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
BackgroundCorrection
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
GcRmaBackgroundCorrection
Directly known subclasses:
public static class GcRmaBackgroundCorrection
extends BackgroundCorrection
This class represents the GCRMA background adjustment function.
GcRmaBackgroundCorrection(..., indicesNegativeControl=NULL, affinities=NULL, type=c("fullmodel", "affinities"), opticalAdjust=TRUE, gsbAdjust=TRUE, gsbParameters=NULL, seed=NULL)
GcRmaBackgroundCorrection(..., indicesNegativeControl=NULL, affinities=NULL, type=c("fullmodel", "affinities"), opticalAdjust=TRUE, gsbAdjust=TRUE, gsbParameters=NULL, seed=NULL)
... |
Arguments passed to the constructor of
|
indicesNegativeControl |
Locations of any negative control
probes (e.g., the anti-genomic controls on the human exon array).
If |
affinities |
A |
type |
Type (flavor) of background correction, which can
be either |
gsbAdjust |
If |
opticalAdjust |
If |
gsbParameters |
Additional argument passed to the internal
|
seed |
An (optional) |
Methods:
process |
- | |
Methods inherited from BackgroundCorrection:
getParameters, process
Methods inherited from ProbeLevelTransform:
getRootPath
Methods inherited from Transform:
getOutputDataSet, getOutputFiles
Methods inherited from AromaTransform:
as.character, findFilesTodo, getAsteriskTags, getExpectedOutputFiles, getExpectedOutputFullnames, getFullName, getInputDataSet, getName, getOutputDataSet, getOutputDataSet0, getOutputFiles, getPath, getRootPath, getTags, isDone, process, setTags
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Ken Simpson, Henrik Bengtsson
[1] Z. Wu, R. Irizarry, R. Gentleman, F.M. Murillo & F. Spencer.
A Model Based Background Adjustment for Oligonucleotide
Expression Arrays, JASA, 2004.
Package: aroma.affymetrix
Class GenericReporter
Object
~~|
~~+--
GenericReporter
Directly known subclasses:
AffymetrixCelSetReporter, AffymetrixFileSetReporter, SpatialReporter
public abstract static class GenericReporter
extends Object
GenericReporter(tags="*", ...)
GenericReporter(tags="*", ...)
tags |
|
... |
Not used. |
Methods:
getFullName |
- | |
getName |
- | |
getPath |
- | |
getTags |
- | |
process |
- | |
setup |
- | |
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.affymetrix
Class GenomeInformation
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
CacheKeyInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
GenomeInformation
Directly known subclasses:
AffymetrixCsvGenomeInformation, DChipGenomeInformation, UgpGenomeInformation
public abstract static class GenomeInformation
extends FileCacheKeyInterface
GenomeInformation(..., .verify=TRUE)
GenomeInformation(..., .verify=TRUE)
... |
Arguments passed to |
.verify |
For internal use only. |
Methods:
byChipType |
- | |
getChipType |
- | |
getChromosomeStats |
- | |
getChromosomes |
- | |
getData |
- | |
getPositions |
- | |
getUnitsOnChromosome |
- | |
getUnitsOnChromosomes |
- | |
nbrOfUnits |
- | |
plotDensity |
- | |
Methods inherited from FileCacheKeyInterface:
getCacheKey
Methods inherited from CacheKeyInterface:
getCacheKey
Methods inherited from GenericDataFile:
as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.affymetrix
Class HetLogAddCnPlm
Object
~~|
~~+--
ParametersInterface
~~~~~~~|
~~~~~~~+--
Model
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
UnitModel
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
MultiArrayUnitModel
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
ProbeLevelModel
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
RmaPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
HetLogAddPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
HetLogAddSnpPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
SnpPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
CnPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
HetLogAddCnPlm
Directly known subclasses:
public abstract static class HetLogAddCnPlm
extends CnPlm
HetLogAddCnPlm(..., combineAlleles=FALSE)
HetLogAddCnPlm(..., combineAlleles=FALSE)
... |
Arguments passed to |
combineAlleles |
If |
Methods:
No methods defined.
Methods inherited from CnPlm:
getCellIndices, getChipEffectSet, getCombineAlleles, getParameters, getProbeAffinityFile, setCombineAlleles
Methods inherited from SnpPlm:
getCellIndices, getChipEffectSet, getMergeStrands, getParameters, getProbeAffinityFile, setMergeStrands
Methods inherited from HetLogAddSnpPlm:
getAsteriskTags
Methods inherited from HetLogAddPlm:
getAsteriskTags, getFitUnitGroupFunction
Methods inherited from RmaPlm:
getAsteriskTags, getCalculateResidualsFunction, getParameters, getRlmFitFunctions
Methods inherited from ProbeLevelModel:
calculateResidualSet, calculateWeights, fit, getAsteriskTags, getCalculateResidualsFunction, getChipEffectSet, getProbeAffinityFile, getResidualSet, getRootPath, getWeightsSet
Methods inherited from MultiArrayUnitModel:
getListOfPriors, setListOfPriors, validate
Methods inherited from UnitModel:
findUnitsTodo, getAsteriskTags, getFitSingleCellUnitFunction, getParameters
Methods inherited from Model:
as.character, fit, getAlias, getAsteriskTags, getDataSet, getFullName, getName, getPath, getRootPath, getTags, setAlias, setTags
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
TO DO.
Henrik Bengtsson
Package: aroma.affymetrix
Class HetLogAddPlm
Object
~~|
~~+--
ParametersInterface
~~~~~~~|
~~~~~~~+--
Model
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
UnitModel
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
MultiArrayUnitModel
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
ProbeLevelModel
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
RmaPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
HetLogAddPlm
Directly known subclasses:
HetLogAddCnPlm, HetLogAddSnpPlm
public abstract static class HetLogAddPlm
extends RmaPlm
This class represents a log-additive model similar to the one described in Irizarry et al (2003), except that the errors may have different variances for different probes.
HetLogAddPlm(...)
HetLogAddPlm(...)
... |
Arguments passed to |
Methods:
No methods defined.
Methods inherited from RmaPlm:
getAsteriskTags, getCalculateResidualsFunction, getParameters, getRlmFitFunctions
Methods inherited from ProbeLevelModel:
calculateResidualSet, calculateWeights, fit, getAsteriskTags, getCalculateResidualsFunction, getChipEffectSet, getProbeAffinityFile, getResidualSet, getRootPath, getWeightsSet
Methods inherited from MultiArrayUnitModel:
getListOfPriors, setListOfPriors, validate
Methods inherited from UnitModel:
findUnitsTodo, getAsteriskTags, getFitSingleCellUnitFunction, getParameters
Methods inherited from Model:
as.character, fit, getAlias, getAsteriskTags, getDataSet, getFullName, getName, getPath, getRootPath, getTags, setAlias, setTags
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.affymetrix
Class HetLogAddSnpPlm
Object
~~|
~~+--
ParametersInterface
~~~~~~~|
~~~~~~~+--
Model
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
UnitModel
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
MultiArrayUnitModel
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
ProbeLevelModel
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
RmaPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
HetLogAddPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
SnpPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
HetLogAddSnpPlm
Directly known subclasses:
HetLogAddCnPlm
public abstract static class HetLogAddSnpPlm
extends SnpPlm
HetLogAddSnpPlm(..., mergeStrands=FALSE)
HetLogAddSnpPlm(..., mergeStrands=FALSE)
... |
Arguments passed to |
mergeStrands |
If |
Methods:
No methods defined.
Methods inherited from SnpPlm:
getCellIndices, getChipEffectSet, getMergeStrands, getParameters, getProbeAffinityFile, setMergeStrands
Methods inherited from HetLogAddPlm:
getAsteriskTags, getFitUnitGroupFunction
Methods inherited from RmaPlm:
getAsteriskTags, getCalculateResidualsFunction, getParameters, getRlmFitFunctions
Methods inherited from ProbeLevelModel:
calculateResidualSet, calculateWeights, fit, getAsteriskTags, getCalculateResidualsFunction, getChipEffectSet, getProbeAffinityFile, getResidualSet, getRootPath, getWeightsSet
Methods inherited from MultiArrayUnitModel:
getListOfPriors, setListOfPriors, validate
Methods inherited from UnitModel:
findUnitsTodo, getAsteriskTags, getFitSingleCellUnitFunction, getParameters
Methods inherited from Model:
as.character, fit, getAlias, getAsteriskTags, getDataSet, getFullName, getName, getPath, getRootPath, getTags, setAlias, setTags
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Robust Multichip Analysis (RMA) reproducing the affy package as far as possible. The RMA method is described in [1].
The algorithm is processed in bounded memory, meaning a very large
number of arrays can be analyzed on also very limited computer systems.
The only limitation is the amount of memory required to load the final
chip-effect estimates into memory (as a ExpressionSet
).
## S3 method for class 'AffymetrixCelSet' justRMA(csR, flavor=c("oligo", "affyPLM"), ..., verbose=FALSE) ## Default S3 method: justRMA(...)
## S3 method for class 'AffymetrixCelSet' justRMA(csR, flavor=c("oligo", "affyPLM"), ..., verbose=FALSE) ## Default S3 method: justRMA(...)
csR |
An |
flavor |
A |
... |
Additional arguments passed to |
verbose |
See |
Returns an annotated ExpressionSet
.
This implementation of the RMA method reproduces justRMA
in affy package quite well. It does so by still using a
constant memory profile, i.e. it is possible to use this implementation
to run RMA on a much large data set than what is possible with
affy. At least 20-50 times more samples should be
doable, if not more.
Henrik Bengtsson
[1] Irizarry et al.
Summaries of Affymetrix GeneChip probe level data.
NAR, 2003, 31, e15.
doRMA
().
Package: aroma.affymetrix
Class LimmaBackgroundCorrection
Object
~~|
~~+--
ParametersInterface
~~~~~~~|
~~~~~~~+--
AromaTransform
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
Transform
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
ProbeLevelTransform
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
BackgroundCorrection
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
LimmaBackgroundCorrection
Directly known subclasses:
NormExpBackgroundCorrection
public static class LimmaBackgroundCorrection
extends BackgroundCorrection
This class represents the various "background" correction methods implemented in the limma package.
LimmaBackgroundCorrection(..., args=NULL, addJitter=FALSE, jitterSd=0.2, seed=6022007)
LimmaBackgroundCorrection(..., args=NULL, addJitter=FALSE, jitterSd=0.2, seed=6022007)
... |
Arguments passed to the constructor of
|
args |
A |
addJitter |
If |
jitterSd |
Standard deviation of the jitter noise added. |
seed |
An (optional) |
By default, only PM signals are background corrected and MMs are left unchanged.
Methods:
process |
- | |
Methods inherited from BackgroundCorrection:
getParameters, process
Methods inherited from ProbeLevelTransform:
getRootPath
Methods inherited from Transform:
getOutputDataSet, getOutputFiles
Methods inherited from AromaTransform:
as.character, findFilesTodo, getAsteriskTags, getExpectedOutputFiles, getExpectedOutputFullnames, getFullName, getInputDataSet, getName, getOutputDataSet, getOutputDataSet0, getOutputFiles, getPath, getRootPath, getTags, isDone, process, setTags
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
The fitting algorithm of the normal+exponential background correction model may not converge if there too many small and discrete signals. To overcome this problem, a small amount of noise may be added to the signals before fitting the model. This is an ad hoc solution that seems to work. However, adding Gaussian noise may generate non-positive signals.
Henrik Bengtsson. Adopted from RmaBackgroundCorrection by Ken Simpson.
Internally, backgroundCorrect
is used.
Package: aroma.affymetrix
Class LinearModelProbeSequenceNormalization
Object
~~|
~~+--
ParametersInterface
~~~~~~~|
~~~~~~~+--
AromaTransform
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
Transform
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
ProbeLevelTransform
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
ProbeLevelTransform3
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AbstractProbeSequenceNormalization
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
LinearModelProbeSequenceNormalization
Directly known subclasses:
BasePositionNormalization
public abstract static class LinearModelProbeSequenceNormalization
extends AbstractProbeSequenceNormalization
This abstract class represents a normalization method that corrects for systematic effects in the probe intensities due to probe-sequence dependent effects that can be modeled using a linear model.
LinearModelProbeSequenceNormalization(...)
LinearModelProbeSequenceNormalization(...)
... |
Arguments passed to the constructor of
|
Methods:
No methods defined.
Methods inherited from AbstractProbeSequenceNormalization:
fitOne, getAromaCellSequenceFile, getParameters, getTargetFile, indexOfMissingSequences, predictOne, process
Methods inherited from ProbeLevelTransform3:
getAsteriskTags, getCellsTo, getCellsToFit, getCellsToUpdate, getParameters, getUnitsTo, getUnitsToFit, getUnitsToUpdate, writeSignals
Methods inherited from ProbeLevelTransform:
getRootPath
Methods inherited from Transform:
getOutputDataSet, getOutputFiles
Methods inherited from AromaTransform:
as.character, findFilesTodo, getAsteriskTags, getExpectedOutputFiles, getExpectedOutputFullnames, getFullName, getInputDataSet, getName, getOutputDataSet, getOutputDataSet0, getOutputFiles, getPath, getRootPath, getTags, isDone, process, setTags
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
This class requires that an aroma probe sequence file is available for the chip type.
The model fitting methods of this class are bounded in memory.
This is done by first building up the normal equations incrementally
in chunks of cells. The generation of normal equations is otherwise
the step that consumes the most memory.
When the normal equations are available, the solve
()
method is used to solve the equations. Note that this algorithm is
still exact.
Henrik Bengtsson
Package: aroma.affymetrix
Class MatNormalization
Object
~~|
~~+--
ParametersInterface
~~~~~~~|
~~~~~~~+--
AromaTransform
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
Transform
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
ProbeLevelTransform
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
ProbeLevelTransform3
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AbstractProbeSequenceNormalization
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
MatNormalization
Directly known subclasses:
public static class MatNormalization
extends AbstractProbeSequenceNormalization
This class represents a normalization method that corrects for systematic effects in the probe intensities due to differences in the number of A, C, G, and T:s and the match scores according to MAT [1].
MatNormalization(..., unitsToFit=NULL, model=c("lm"), nbrOfBins=200)
MatNormalization(..., unitsToFit=NULL, model=c("lm"), nbrOfBins=200)
... |
Arguments passed to the constructor of
|
unitsToFit |
The units from which the normalization curve should
be estimated. If |
model |
A |
nbrOfBins |
The number of bins to use for the variance smoothing step. |
Methods:
process |
- | |
Methods inherited from AbstractProbeSequenceNormalization:
fitOne, getAromaCellSequenceFile, getParameters, getTargetFile, indexOfMissingSequences, predictOne, process
Methods inherited from ProbeLevelTransform3:
getAsteriskTags, getCellsTo, getCellsToFit, getCellsToUpdate, getParameters, getUnitsTo, getUnitsToFit, getUnitsToUpdate, writeSignals
Methods inherited from ProbeLevelTransform:
getRootPath
Methods inherited from Transform:
getOutputDataSet, getOutputFiles
Methods inherited from AromaTransform:
as.character, findFilesTodo, getAsteriskTags, getExpectedOutputFiles, getExpectedOutputFullnames, getFullName, getInputDataSet, getName, getOutputDataSet, getOutputDataSet0, getOutputFiles, getPath, getRootPath, getTags, isDone, process, setTags
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
This class requires that an aroma probe sequence file and aroma match scores file is available for the chip type.
Mark Robinson
[1] Johnson WE, Li W, Meyer CA, Gottardo R, Carroll JS, Brown M, Liu XS. Model-based analysis of tiling-arrays for ChIP-chip, PNAS, 2006.
Package: aroma.affymetrix
Class MatSmoothing
Object
~~|
~~+--
ParametersInterface
~~~~~~~|
~~~~~~~+--
AromaTransform
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
Transform
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
ProbeLevelTransform
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
MatSmoothing
Directly known subclasses:
public static class MatSmoothing
extends ProbeLevelTransform
This class represents a function for smoothing data with a trimmed mean.
MatSmoothing(..., design=NULL, probeWindow=300, nProbes=10, meanTrim=0.1)
MatSmoothing(..., design=NULL, probeWindow=300, nProbes=10, meanTrim=0.1)
... |
Arguments passed to |
design |
A design |
probeWindow |
Bandwidth to use. Effectively the width is 2*probeWindow since it looks probeWindow bases in either direction. |
nProbes |
The minimum number of probes to calculate a MAT score for. |
meanTrim |
The amount of trimming of the mean in [0,0.5]. |
Methods:
process |
- | |
Methods inherited from ProbeLevelTransform:
getRootPath
Methods inherited from Transform:
getOutputDataSet, getOutputFiles
Methods inherited from AromaTransform:
as.character, findFilesTodo, getAsteriskTags, getExpectedOutputFiles, getExpectedOutputFullnames, getFullName, getInputDataSet, getName, getOutputDataSet, getOutputDataSet0, getOutputFiles, getPath, getRootPath, getTags, isDone, process, setTags
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Mark Robinson, Henrik Bengtsson
Package: aroma.affymetrix
Class MbeiCnPlm
Object
~~|
~~+--
ParametersInterface
~~~~~~~|
~~~~~~~+--
Model
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
UnitModel
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
MultiArrayUnitModel
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
ProbeLevelModel
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
MbeiPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
MbeiSnpPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
SnpPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
CnPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
MbeiCnPlm
Directly known subclasses:
public abstract static class MbeiCnPlm
extends CnPlm
MbeiCnPlm(..., combineAlleles=FALSE)
MbeiCnPlm(..., combineAlleles=FALSE)
... |
Arguments passed to |
combineAlleles |
If |
Methods:
No methods defined.
Methods inherited from CnPlm:
getCellIndices, getChipEffectSet, getCombineAlleles, getParameters, getProbeAffinityFile, setCombineAlleles
Methods inherited from SnpPlm:
getCellIndices, getChipEffectSet, getMergeStrands, getParameters, getProbeAffinityFile, setMergeStrands
Methods inherited from MbeiSnpPlm:
getAsteriskTags
Methods inherited from MbeiPlm:
getAsteriskTags, getFitUnitGroupFunction
Methods inherited from ProbeLevelModel:
calculateResidualSet, calculateWeights, fit, getAsteriskTags, getCalculateResidualsFunction, getChipEffectSet, getProbeAffinityFile, getResidualSet, getRootPath, getWeightsSet
Methods inherited from MultiArrayUnitModel:
getListOfPriors, setListOfPriors, validate
Methods inherited from UnitModel:
findUnitsTodo, getAsteriskTags, getFitSingleCellUnitFunction, getParameters
Methods inherited from Model:
as.character, fit, getAlias, getAsteriskTags, getDataSet, getFullName, getName, getPath, getRootPath, getTags, setAlias, setTags
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.affymetrix
Class MbeiPlm
Object
~~|
~~+--
ParametersInterface
~~~~~~~|
~~~~~~~+--
Model
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
UnitModel
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
MultiArrayUnitModel
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
ProbeLevelModel
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
MbeiPlm
Directly known subclasses:
MbeiCnPlm, MbeiSnpPlm
public abstract static class MbeiPlm
extends ProbeLevelModel
This class represents the model-based expression indexes (MBEI) multiplicative model in Li & Wong (2001).
MbeiPlm(...)
MbeiPlm(...)
... |
Arguments passed to |
Methods:
No methods defined.
Methods inherited from ProbeLevelModel:
calculateResidualSet, calculateWeights, fit, getAsteriskTags, getCalculateResidualsFunction, getChipEffectSet, getProbeAffinityFile, getResidualSet, getRootPath, getWeightsSet
Methods inherited from MultiArrayUnitModel:
getListOfPriors, setListOfPriors, validate
Methods inherited from UnitModel:
findUnitsTodo, getAsteriskTags, getFitSingleCellUnitFunction, getParameters
Methods inherited from Model:
as.character, fit, getAlias, getAsteriskTags, getDataSet, getFullName, getName, getPath, getRootPath, getTags, setAlias, setTags
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
For a single unit group, the multiplicative model is:
where are the chip effects for arrays
,
and
are the probe affinities for probes
.
The
are zero-mean noise with equal variance.
To make to parameters identifiable, the constraint
is added.
Henrik Bengtsson
Li, C. and Wong, W.H. (2001), Genome Biology 2, 1-11.
Li, C. and Wong, W.H. (2001), Proc. Natl. Acad. Sci USA 98, 31-36.
Internally fit.li.wong
is used.
Package: aroma.affymetrix
Class MbeiSnpPlm
Object
~~|
~~+--
ParametersInterface
~~~~~~~|
~~~~~~~+--
Model
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
UnitModel
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
MultiArrayUnitModel
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
ProbeLevelModel
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
MbeiPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
SnpPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
MbeiSnpPlm
Directly known subclasses:
MbeiCnPlm
public abstract static class MbeiSnpPlm
extends SnpPlm
MbeiSnpPlm(..., mergeStrands=FALSE)
MbeiSnpPlm(..., mergeStrands=FALSE)
... |
Arguments passed to |
mergeStrands |
If |
Methods:
No methods defined.
Methods inherited from SnpPlm:
getCellIndices, getChipEffectSet, getMergeStrands, getParameters, getProbeAffinityFile, setMergeStrands
Methods inherited from MbeiPlm:
getAsteriskTags, getFitUnitGroupFunction
Methods inherited from ProbeLevelModel:
calculateResidualSet, calculateWeights, fit, getAsteriskTags, getCalculateResidualsFunction, getChipEffectSet, getProbeAffinityFile, getResidualSet, getRootPath, getWeightsSet
Methods inherited from MultiArrayUnitModel:
getListOfPriors, setListOfPriors, validate
Methods inherited from UnitModel:
findUnitsTodo, getAsteriskTags, getFitSingleCellUnitFunction, getParameters
Methods inherited from Model:
as.character, fit, getAlias, getAsteriskTags, getDataSet, getFullName, getName, getPath, getRootPath, getTags, setAlias, setTags
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.affymetrix
Class Model
Object
~~|
~~+--
ParametersInterface
~~~~~~~|
~~~~~~~+--
Model
Directly known subclasses:
AffineCnPlm, AffinePlm, AffineSnpPlm, AlleleSummation, AvgCnPlm, AvgPlm, AvgSnpPlm, CrlmmModel, ExonRmaPlm, FirmaModel, HetLogAddCnPlm, HetLogAddPlm, HetLogAddSnpPlm, MbeiCnPlm, MbeiPlm, MbeiSnpPlm, MultiArrayUnitModel, ProbeLevelModel, RmaCnPlm, RmaPlm, RmaSnpPlm, SingleArrayUnitModel, UnitModel
public abstract static class Model
extends ParametersInterface
This class is abstract and represents a generic model that applies to a data set.
Model(dataSet=NULL, tags="*", ..., .onUnknownArgs=c("error", "warning", "ignore"))
Model(dataSet=NULL, tags="*", ..., .onUnknownArgs=c("error", "warning", "ignore"))
dataSet |
The data set to which this model should be fitted. |
tags |
A |
... |
Not used. |
.onUnknownArgs |
A |
Methods:
fit |
- | |
getAsteriskTags |
- | |
getDataSet |
- | |
getFullName |
- | |
getName |
- | |
getPath |
- | |
getTags |
- | |
setTags |
- | |
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.affymetrix
Class MultiArrayUnitModel
Object
~~|
~~+--
ParametersInterface
~~~~~~~|
~~~~~~~+--
Model
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
UnitModel
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
MultiArrayUnitModel
Directly known subclasses:
AffineCnPlm, AffinePlm, AffineSnpPlm, AvgCnPlm, AvgPlm, AvgSnpPlm, ExonRmaPlm, HetLogAddCnPlm, HetLogAddPlm, HetLogAddSnpPlm, MbeiCnPlm, MbeiPlm, MbeiSnpPlm, ProbeLevelModel, RmaCnPlm, RmaPlm, RmaSnpPlm
public abstract static class MultiArrayUnitModel
extends UnitModel
This abstract class represents a unit model that fits one model per unit based on signals for all arrays in the data set. The nature of a multi-array unit model is that all arrays must be available at the time of the fit and the estimated parameters will depend on the data from all arrays. Thus, if the signals in one array changes the model has to be refitted.
MultiArrayUnitModel(..., listOfPriors=NULL)
MultiArrayUnitModel(..., listOfPriors=NULL)
... |
Arguments passed to |
listOfPriors |
A |
Methods:
getListOfPriors |
- | |
setListOfPriors |
- | |
Methods inherited from UnitModel:
findUnitsTodo, getAsteriskTags, getFitSingleCellUnitFunction, getParameters
Methods inherited from Model:
as.character, fit, getAlias, getAsteriskTags, getDataSet, getFullName, getName, getPath, getRootPath, getTags, setAlias, setTags
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.affymetrix
Class NormExpBackgroundCorrection
Object
~~|
~~+--
ParametersInterface
~~~~~~~|
~~~~~~~+--
AromaTransform
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
Transform
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
ProbeLevelTransform
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
BackgroundCorrection
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
LimmaBackgroundCorrection
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
NormExpBackgroundCorrection
Directly known subclasses:
public static class NormExpBackgroundCorrection
extends LimmaBackgroundCorrection
This class represents the normal exponential background correction model. Estimators of the limma package is used.
NormExpBackgroundCorrection(..., method=c("rma", "saddle", "mle"))
NormExpBackgroundCorrection(..., method=c("rma", "saddle", "mle"))
... |
Arguments passed to the constructor of
|
method |
The estimator used, cf. argument |
Methods:
No methods defined.
Methods inherited from LimmaBackgroundCorrection:
getAsteriskTags, getParameters, process
Methods inherited from BackgroundCorrection:
getParameters, process
Methods inherited from ProbeLevelTransform:
getRootPath
Methods inherited from Transform:
getOutputDataSet, getOutputFiles
Methods inherited from AromaTransform:
as.character, findFilesTodo, getAsteriskTags, getExpectedOutputFiles, getExpectedOutputFullnames, getFullName, getInputDataSet, getName, getOutputDataSet, getOutputDataSet0, getOutputFiles, getPath, getRootPath, getTags, isDone, process, setTags
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Internally, backgroundCorrect
is used.
Package: aroma.affymetrix
Class OpticalBackgroundCorrection
Object
~~|
~~+--
ParametersInterface
~~~~~~~|
~~~~~~~+--
AromaTransform
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
Transform
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
ProbeLevelTransform
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
BackgroundCorrection
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
OpticalBackgroundCorrection
Directly known subclasses:
public static class OpticalBackgroundCorrection
extends BackgroundCorrection
This class represents "optical" background adjustment.
OpticalBackgroundCorrection(..., minimum=1)
OpticalBackgroundCorrection(..., minimum=1)
... |
Arguments passed to the constructor of
|
minimum |
The minimum signal allowed after adjustment. |
Methods:
process |
- | |
Methods inherited from BackgroundCorrection:
getParameters, process
Methods inherited from ProbeLevelTransform:
getRootPath
Methods inherited from Transform:
getOutputDataSet, getOutputFiles
Methods inherited from AromaTransform:
as.character, findFilesTodo, getAsteriskTags, getExpectedOutputFiles, getExpectedOutputFullnames, getFullName, getInputDataSet, getName, getOutputDataSet, getOutputDataSet0, getOutputFiles, getPath, getRootPath, getTags, isDone, process, setTags
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Ken Simpson
Package: aroma.affymetrix
Class ParameterCelFile
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
CacheKeyInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
AromaMicroarrayDataFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixCelFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
ParametersInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
ParameterCelFile
Directly known subclasses:
ChipEffectFile, CnChipEffectFile, CnProbeAffinityFile, ExonChipEffectFile, ExonProbeAffinityFile, FirmaFile, ProbeAffinityFile, ResidualFile, SnpChipEffectFile, SnpProbeAffinityFile, WeightsFile
public abstract static class ParameterCelFile
extends ParametersInterface
A ParameterCelFile object represents parameter estimates.
ParameterCelFile(..., encodeFunction=NULL, decodeFunction=NULL)
ParameterCelFile(..., encodeFunction=NULL, decodeFunction=NULL)
... |
Arguments passed to |
encodeFunction |
|
decodeFunction |
Methods:
extractDataFrame |
- | |
extractMatrix |
- | |
readUnits |
- | |
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from AffymetrixCelFile:
allocateFromCdf, as.character, clone, createFrom, extractMatrix, fromFile, getAm, getCdf, getExtensionPattern, getFileFormat, getImage, getUnitNamesFile, getUnitTypesFile, highlight, image270, nbrOfCells, plotDensity, plotImage, plotMvsA, plotMvsX, range, setCdf, smoothScatterMvsA, writeImage
Methods inherited from AromaPlatformInterface:
getAromaPlatform, getAromaUflFile, getAromaUgpFile, getChipType, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith
Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags
Methods inherited from FileCacheKeyInterface:
getCacheKey
Methods inherited from CacheKeyInterface:
getCacheKey
Methods inherited from GenericDataFile:
as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
The idea behind this class is store data fields which by nature have one value per probe (per field) in CEL files. A perfect example is to store probe-affinity estimates and their standard deviations. There is one probe affinity per probe so the structure of a CEL file (and its coupled CDF file) is well suited to read/write such information.
Consider a unit group with L probes. A CEL file stores
intensities
(L floats), stdvs
(L floats), and
pixels
(L integers). Thus, for each probe l=1,...,L, a
(float, float, integer) tuple is stored. We can use this for any
information we want. If we want a slightly different structure,
we can choose to encode/decode our structure/information to fit the
structure of the CEL file. This abstract class provides transparent
methods for encoding and decoding such information through methods
encodeUnitGroup()
and decodeUnitGroup()
.
By subclassing you can implement different types of data structures.
Henrik Bengtsson
Package: aroma.affymetrix
Class ParameterCelSet
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFileSet
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
AromaMicroarrayDataSet
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixFileSet
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixCelSet
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
ParametersInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
ParameterCelSet
Directly known subclasses:
ChipEffectSet, CnChipEffectSet, ExonChipEffectSet, FirmaSet, SnpChipEffectSet
public static class ParameterCelSet
extends ParametersInterface
A ParameterCelSet object represents a set of ParameterCelFile
:s.
ParameterCelSet(...)
ParameterCelSet(...)
... |
Arguments passed to |
Methods:
extractDataFrame |
- | |
extractMatrix |
- | |
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from AffymetrixCelSet:
append, as, as.AffymetrixCelSet, as.character, averageQuantile, byName, byPath, clone, convertToUnique, doCRMAv1, doCRMAv2, doFIRMA, doGCRMA, doRMA, extractAffyBatch, extractFeatureSet, extractMatrix, extractSnpFeatureSet, findByName, getAverage, getAverageAsinh, getAverageFile, getAverageLog, getCdf, getChipType, getData, getIntensities, getPlatform, getTimestamps, getUnitGroupCellMap, getUnitIntensities, getUnitNamesFile, getUnitTypesFile, isDuplicated, justRMA, justSNPRMA, nbrOfArrays, normalizeQuantile, plotDensity, range, readUnits, setCdf, update2, writeSgr
Methods inherited from AffymetrixFileSet:
as, as.AffymetrixFileSet, byPath, getDefaultFullName
Methods inherited from AromaPlatformInterface:
getAromaPlatform, getAromaUflFile, getAromaUgpFile, getChipType, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith
Methods inherited from AromaMicroarrayDataSet:
as.AromaMicroarrayDataSetList, as.AromaMicroarrayDataSetTuple, getAromaFullNameTranslatorSet, getAverageFile, getChipType, getDefaultFullName, getPlatform, setAttributesBy, setAttributesBySampleAnnotationFile, setAttributesBySampleAnnotationSet, validate
Methods inherited from GenericDataFileSet:
[, [[, anyDuplicated, anyNA, append, appendFiles, appendFullNamesTranslator, appendFullNamesTranslatorByNULL, appendFullNamesTranslatorByTabularTextFile, appendFullNamesTranslatorByTabularTextFileSet, appendFullNamesTranslatorBydata.frame, appendFullNamesTranslatorByfunction, appendFullNamesTranslatorBylist, as.character, as.list, byName, byPath, c, clearCache, clearFullNamesTranslator, clone, copyTo, dsApplyInPairs, duplicated, equals, extract, findByName, findDuplicated, getChecksum, getChecksumFileSet, getChecksumObjects, getDefaultFullName, getFile, getFileClass, getFileSize, getFiles, getFullNames, getNames, getOneFile, getPath, getPathnames, getSubdirs, gunzip, gzip, hasFile, indexOf, is.na, names, nbrOfFiles, rep, resetFullNames, setFullNamesTranslator, sortBy, unique, update2, updateFullName, updateFullNames, validate, getFullNameTranslatorSet, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.affymetrix
Class ProbeAffinityFile
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
CacheKeyInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
AromaMicroarrayDataFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixCelFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
ParametersInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
ParameterCelFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
ProbeAffinityFile
Directly known subclasses:
CnProbeAffinityFile, ExonProbeAffinityFile, SnpProbeAffinityFile
public abstract static class ProbeAffinityFile
extends ParameterCelFile
This class represents estimates of probe affinities in probe-level models.
ProbeAffinityFile(..., probeModel=c("pm", "mm", "pm-mm", "min1(pm-mm)", "pm+mm"))
ProbeAffinityFile(..., probeModel=c("pm", "mm", "pm-mm", "min1(pm-mm)", "pm+mm"))
... |
Arguments passed to |
probeModel |
The specific type of probe model. |
Methods:
readUnits |
- | |
Methods inherited from ParameterCelFile:
extractDataFrame, extractMatrix, readUnits
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from AffymetrixCelFile:
allocateFromCdf, as.character, clone, createFrom, extractMatrix, fromFile, getAm, getCdf, getExtensionPattern, getFileFormat, getImage, getUnitNamesFile, getUnitTypesFile, highlight, image270, nbrOfCells, plotDensity, plotImage, plotMvsA, plotMvsX, range, setCdf, smoothScatterMvsA, writeImage
Methods inherited from AromaPlatformInterface:
getAromaPlatform, getAromaUflFile, getAromaUgpFile, getChipType, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith
Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags
Methods inherited from FileCacheKeyInterface:
getCacheKey
Methods inherited from CacheKeyInterface:
getCacheKey
Methods inherited from GenericDataFile:
as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
An object of this class is typically obtained through the
getProbeAffinityFile()
method for the ProbeLevelModel
class.
Package: aroma.affymetrix
Class ProbeLevelModel
Object
~~|
~~+--
ParametersInterface
~~~~~~~|
~~~~~~~+--
Model
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
UnitModel
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
MultiArrayUnitModel
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
ProbeLevelModel
Directly known subclasses:
AffineCnPlm, AffinePlm, AffineSnpPlm, AvgCnPlm, AvgPlm, AvgSnpPlm, ExonRmaPlm, HetLogAddCnPlm, HetLogAddPlm, HetLogAddSnpPlm, MbeiCnPlm, MbeiPlm, MbeiSnpPlm, RmaCnPlm, RmaPlm, RmaSnpPlm
public abstract static class ProbeLevelModel
extends MultiArrayUnitModel
This abstract class represents a probe-level model (PLM) as defined by the affyPLM package: "A [...] PLM is a model that is fit to probe-intensity data. More specifically, it is where we fit a model with probe level and chip level parameters on a probeset by probeset basis", where the more general case for a probeset is a unit group in Affymetrix CDF terms.
ProbeLevelModel(..., standardize=TRUE)
ProbeLevelModel(..., standardize=TRUE)
... |
Arguments passed to |
standardize |
If |
In order to minimize the risk for mistakes, but also to be able compare results from different PLMs, all PLM subclasses must meet the following criteria:
All parameter estimates must be (stored and returned) on the
intensity scale, e.g. log-additive models such as RmaPlm
have to transform the parameters on the log-scale to the intensity
scale.
The probe-affinity estimates for a unit group
must be constrained such that
,
or equivalently if
,
.
Note that the above probe-affinity constraint guarantees that the estimated chip effects across models are on the same scale.
Methods:
fit |
- | |
getChipEffectSet |
- | |
getProbeAffinityFile |
- | |
getResidualSet |
- | |
getWeightsSet |
- | |
Methods inherited from MultiArrayUnitModel:
getListOfPriors, setListOfPriors, validate
Methods inherited from UnitModel:
findUnitsTodo, getAsteriskTags, getFitSingleCellUnitFunction, getParameters
Methods inherited from Model:
as.character, fit, getAlias, getAsteriskTags, getDataSet, getFullName, getName, getPath, getRootPath, getTags, setAlias, setTags
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
For more details on probe-level models, please see the preprocessCore package.
Package: aroma.affymetrix
Class ProbeLevelTransform
Object
~~|
~~+--
ParametersInterface
~~~~~~~|
~~~~~~~+--
AromaTransform
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
Transform
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
ProbeLevelTransform
Directly known subclasses:
AbstractProbeSequenceNormalization, AllelicCrosstalkCalibration, BackgroundCorrection, BaseCountNormalization, BasePositionNormalization, DChipQuantileNormalization, GcRmaBackgroundCorrection, LimmaBackgroundCorrection, LinearModelProbeSequenceNormalization, MatNormalization, MatSmoothing, NormExpBackgroundCorrection, OpticalBackgroundCorrection, ProbeLevelTransform3, QuantileNormalization, ReseqCrosstalkCalibration, RmaBackgroundCorrection, ScaleNormalization, ScaleNormalization3, SpatialRowColumnNormalization, UnitTypeScaleNormalization
public abstract static class ProbeLevelTransform
extends Transform
This abstract class represents a transformation methods that transforms probe-level signals, typically intensities.
ProbeLevelTransform(...)
ProbeLevelTransform(...)
... |
Arguments passed to the constructor of |
Subclasses must implement the process()
method.
Methods:
No methods defined.
Methods inherited from Transform:
getOutputDataSet, getOutputFiles
Methods inherited from AromaTransform:
as.character, findFilesTodo, getAsteriskTags, getExpectedOutputFiles, getExpectedOutputFullnames, getFullName, getInputDataSet, getName, getOutputDataSet, getOutputDataSet0, getOutputFiles, getPath, getRootPath, getTags, isDone, process, setTags
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.affymetrix
Class ProbeLevelTransform3
Object
~~|
~~+--
ParametersInterface
~~~~~~~|
~~~~~~~+--
AromaTransform
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
Transform
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
ProbeLevelTransform
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
ProbeLevelTransform3
Directly known subclasses:
AbstractProbeSequenceNormalization, BaseCountNormalization, BasePositionNormalization, LinearModelProbeSequenceNormalization, MatNormalization, ScaleNormalization3, UnitTypeScaleNormalization
public abstract static class ProbeLevelTransform3
extends ProbeLevelTransform
This abstract class is specialized from ProbeLevelTransform
and
provides methods to identify subsets and types of probes that are used
for fitting and/or updating the signals.
ProbeLevelTransform3(dataSet=NULL, ..., unitsToFit="-XY", typesToFit=typesToUpdate, unitsToUpdate=NULL, typesToUpdate="pm", shift=0)
ProbeLevelTransform3(dataSet=NULL, ..., unitsToFit="-XY", typesToFit=typesToUpdate, unitsToUpdate=NULL, typesToUpdate="pm", shift=0)
dataSet |
|
... |
Arguments passed to the constructor of
|
unitsToFit |
The units from which the normalization curve should
be estimated. If |
typesToFit |
Types of probes to be used when fitting the model. |
unitsToUpdate |
The units to be updated.
If |
typesToUpdate |
Types of probes to be updated. |
shift |
An optional amount to shift data before fitting and updating. |
Methods:
No methods defined.
Methods inherited from ProbeLevelTransform:
getRootPath
Methods inherited from Transform:
getOutputDataSet, getOutputFiles
Methods inherited from AromaTransform:
as.character, findFilesTodo, getAsteriskTags, getExpectedOutputFiles, getExpectedOutputFullnames, getFullName, getInputDataSet, getName, getOutputDataSet, getOutputDataSet0, getOutputFiles, getPath, getRootPath, getTags, isDone, process, setTags
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.affymetrix
Class QualityAssessmentFile
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
CacheKeyInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
AromaMicroarrayDataFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixCelFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
QualityAssessmentFile
Directly known subclasses:
public abstract static class QualityAssessmentFile
extends AffymetrixCelFile
This class represents probe-level QC information (residuals, weights, etc.)
QualityAssessmentFile(...)
QualityAssessmentFile(...)
... |
Arguments passed to |
Methods:
findUnitsTodo |
- | |
Methods inherited from AffymetrixCelFile:
allocateFromCdf, as.character, clone, createFrom, extractMatrix, fromFile, getAm, getCdf, getExtensionPattern, getFileFormat, getImage, getUnitNamesFile, getUnitTypesFile, highlight, image270, nbrOfCells, plotDensity, plotImage, plotMvsA, plotMvsX, range, setCdf, smoothScatterMvsA, writeImage
Methods inherited from AromaPlatformInterface:
getAromaPlatform, getAromaUflFile, getAromaUgpFile, getChipType, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith
Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags
Methods inherited from FileCacheKeyInterface:
getCacheKey
Methods inherited from CacheKeyInterface:
getCacheKey
Methods inherited from GenericDataFile:
as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Ken Simpson
An object of this class is typically part of a QualityAssessmentSet
.
Package: aroma.affymetrix
Class QualityAssessmentModel
Object
~~|
~~+--
QualityAssessmentModel
Directly known subclasses:
public static class QualityAssessmentModel
extends Object
QualityAssessmentModel(plm=NULL, tags="*", ...)
QualityAssessmentModel(plm=NULL, tags="*", ...)
plm |
|
tags |
|
... |
Not used. |
Methods:
getChipEffectSet |
- | |
getDataSet |
- | |
getFullName |
- | |
getName |
- | |
getPath |
- | |
getPlm |
- | |
getResiduals |
- | |
getTags |
- | |
getWeights |
- | |
nbrOfArrays |
- | |
plotNuse |
- | |
plotRle |
- | |
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Ken Simpson, Henrik Bengtsson
Package: aroma.affymetrix
Class QualityAssessmentSet
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFileSet
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
AromaMicroarrayDataSet
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixFileSet
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixCelSet
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
QualityAssessmentSet
Directly known subclasses:
public static class QualityAssessmentSet
extends AffymetrixCelSet
QualityAssessmentSet(...)
QualityAssessmentSet(...)
... |
Arguments passed to constructor of |
Methods:
No methods defined.
Methods inherited from AffymetrixCelSet:
append, as, as.AffymetrixCelSet, as.character, averageQuantile, byName, byPath, clone, convertToUnique, doCRMAv1, doCRMAv2, doFIRMA, doGCRMA, doRMA, extractAffyBatch, extractFeatureSet, extractMatrix, extractSnpFeatureSet, findByName, getAverage, getAverageAsinh, getAverageFile, getAverageLog, getCdf, getChipType, getData, getIntensities, getPlatform, getTimestamps, getUnitGroupCellMap, getUnitIntensities, getUnitNamesFile, getUnitTypesFile, isDuplicated, justRMA, justSNPRMA, nbrOfArrays, normalizeQuantile, plotDensity, range, readUnits, setCdf, update2, writeSgr
Methods inherited from AffymetrixFileSet:
as, as.AffymetrixFileSet, byPath, getDefaultFullName
Methods inherited from AromaPlatformInterface:
getAromaPlatform, getAromaUflFile, getAromaUgpFile, getChipType, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith
Methods inherited from AromaMicroarrayDataSet:
as.AromaMicroarrayDataSetList, as.AromaMicroarrayDataSetTuple, getAromaFullNameTranslatorSet, getAverageFile, getChipType, getDefaultFullName, getPlatform, setAttributesBy, setAttributesBySampleAnnotationFile, setAttributesBySampleAnnotationSet, validate
Methods inherited from GenericDataFileSet:
[, [[, anyDuplicated, anyNA, append, appendFiles, appendFullNamesTranslator, appendFullNamesTranslatorByNULL, appendFullNamesTranslatorByTabularTextFile, appendFullNamesTranslatorByTabularTextFileSet, appendFullNamesTranslatorBydata.frame, appendFullNamesTranslatorByfunction, appendFullNamesTranslatorBylist, as.character, as.list, byName, byPath, c, clearCache, clearFullNamesTranslator, clone, copyTo, dsApplyInPairs, duplicated, equals, extract, findByName, findDuplicated, getChecksum, getChecksumFileSet, getChecksumObjects, getDefaultFullName, getFile, getFileClass, getFileSize, getFiles, getFullNames, getNames, getOneFile, getPath, getPathnames, getSubdirs, gunzip, gzip, hasFile, indexOf, is.na, names, nbrOfFiles, rep, resetFullNames, setFullNamesTranslator, sortBy, unique, update2, updateFullName, updateFullNames, validate, getFullNameTranslatorSet, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Ken Simpson
Package: aroma.affymetrix
Class QuantileNormalization
Object
~~|
~~+--
ParametersInterface
~~~~~~~|
~~~~~~~+--
AromaTransform
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
Transform
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
ProbeLevelTransform
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
QuantileNormalization
Directly known subclasses:
DChipQuantileNormalization
public static class QuantileNormalization
extends ProbeLevelTransform
This class represents a normalization function that transforms the probe-level signals towards the same empirical distribution.
QuantileNormalization(..., subsetToUpdate=NULL, typesToUpdate=NULL, targetDistribution=NULL, subsetToAvg=subsetToUpdate, typesToAvg=typesToUpdate)
QuantileNormalization(..., subsetToUpdate=NULL, typesToUpdate=NULL, targetDistribution=NULL, subsetToAvg=subsetToUpdate, typesToAvg=typesToUpdate)
... |
Arguments passed to the constructor of
|
subsetToUpdate |
The probes to be updated.
If |
typesToUpdate |
Types of probes to be updated. |
targetDistribution |
A |
subsetToAvg |
The probes to calculate average empirical
distribution over. If a single |
typesToAvg |
Types of probes to be used when calculating the
average empirical distribution.
If |
Methods:
process |
- | |
Methods inherited from ProbeLevelTransform:
getRootPath
Methods inherited from Transform:
getOutputDataSet, getOutputFiles
Methods inherited from AromaTransform:
as.character, findFilesTodo, getAsteriskTags, getExpectedOutputFiles, getExpectedOutputFullnames, getFullName, getInputDataSet, getName, getOutputDataSet, getOutputDataSet0, getOutputFiles, getPath, getRootPath, getTags, isDone, process, setTags
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
## Not run: for (zzz in 0) { # Setup verbose output verbose <- Arguments$getVerbose(-2) timestampOn(verbose) # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Define an example dataset # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Find any dataset path <- NULL if (is.null(path)) break ds <- AffymetrixCelSet$fromFiles(path) print(ds) # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Normalization # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - norm <- QuantileNormalization(ds, subsetToAvg=1/3) dsQN <- process(norm, verbose=verbose) print(dsQN) } # for (zzz in 0) rm(zzz) ## End(Not run)
## Not run: for (zzz in 0) { # Setup verbose output verbose <- Arguments$getVerbose(-2) timestampOn(verbose) # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Define an example dataset # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Find any dataset path <- NULL if (is.null(path)) break ds <- AffymetrixCelSet$fromFiles(path) print(ds) # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Normalization # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - norm <- QuantileNormalization(ds, subsetToAvg=1/3) dsQN <- process(norm, verbose=verbose) print(dsQN) } # for (zzz in 0) rm(zzz) ## End(Not run)
Package: aroma.affymetrix
Class ReseqCrosstalkCalibration
Object
~~|
~~+--
ParametersInterface
~~~~~~~|
~~~~~~~+--
AromaTransform
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
Transform
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
ProbeLevelTransform
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
ReseqCrosstalkCalibration
Directly known subclasses:
public static class ReseqCrosstalkCalibration
extends ProbeLevelTransform
This class represents a calibration function that transforms the probe-level signals such that the signals from the four nucleotides (A, C, G, T) are orthogonal.
ReseqCrosstalkCalibration(dataSet=NULL, ..., targetAvg=2200, subsetToAvg=NULL, mergeGroups=FALSE, flavor=c("sfit", "expectile"), alpha=c(0.1, 0.075, 0.05, 0.03, 0.01), q=2, Q=98)
ReseqCrosstalkCalibration(dataSet=NULL, ..., targetAvg=2200, subsetToAvg=NULL, mergeGroups=FALSE, flavor=c("sfit", "expectile"), alpha=c(0.1, 0.075, 0.05, 0.03, 0.01), q=2, Q=98)
dataSet |
An |
... |
Arguments passed to the constructor of
|
targetAvg |
The signal(s) that the average of the sum of the probe quartets should have after calibration. |
subsetToAvg |
The indices of the cells (taken as the intersect of
existing indices) used to calculate average in order to rescale to
the target average. If |
mergeGroups |
A |
flavor |
A |
alpha , q , Q
|
Additional arguments passed to
|
Methods:
process |
- | |
Methods inherited from ProbeLevelTransform:
getRootPath
Methods inherited from Transform:
getOutputDataSet, getOutputFiles
Methods inherited from AromaTransform:
as.character, findFilesTodo, getAsteriskTags, getExpectedOutputFiles, getExpectedOutputFullnames, getFullName, getInputDataSet, getName, getOutputDataSet, getOutputDataSet0, getOutputFiles, getPath, getRootPath, getTags, isDone, process, setTags
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.affymetrix
Class ResidualFile
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
CacheKeyInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
AromaMicroarrayDataFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixCelFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
ParametersInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
ParameterCelFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
ResidualFile
Directly known subclasses:
public abstract static class ResidualFile
extends ParameterCelFile
This class represents estimates of residuals in the probe-level models.
ResidualFile(..., probeModel=c("pm"))
ResidualFile(..., probeModel=c("pm"))
... |
Arguments passed to |
probeModel |
The specific type of model, e.g. |
Methods:
findUnitsTodo |
- | |
getImage |
- | |
readUnits |
- | |
writeImage |
- | |
Methods inherited from ParameterCelFile:
extractDataFrame, extractMatrix, readUnits
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from AffymetrixCelFile:
allocateFromCdf, as.character, clone, createFrom, extractMatrix, fromFile, getAm, getCdf, getExtensionPattern, getFileFormat, getImage, getUnitNamesFile, getUnitTypesFile, highlight, image270, nbrOfCells, plotDensity, plotImage, plotMvsA, plotMvsX, range, setCdf, smoothScatterMvsA, writeImage
Methods inherited from AromaPlatformInterface:
getAromaPlatform, getAromaUflFile, getAromaUgpFile, getChipType, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith
Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags
Methods inherited from FileCacheKeyInterface:
getCacheKey
Methods inherited from CacheKeyInterface:
getCacheKey
Methods inherited from GenericDataFile:
as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Ken Simpson, Henrik Bengtsson
An object of this class is typically obtained through the
getResidualSet()
method for the ProbeLevelModel
class.
An object of this class is typically part of a ResidualSet
.
Package: aroma.affymetrix
Class ResidualSet
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFileSet
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
AromaMicroarrayDataSet
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixFileSet
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixCelSet
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
ParametersInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
ResidualSet
Directly known subclasses:
public static class ResidualSet
extends ParametersInterface
This class represents probe-level residuals from probe-level models.
ResidualSet(..., probeModel=c("pm"))
ResidualSet(..., probeModel=c("pm"))
... |
Arguments passed to |
probeModel |
The specific type of model, e.g. |
Methods:
findUnitsTodo |
- | |
getAverageFile |
- | |
getCellIndices |
- | |
readUnits |
- | |
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from AffymetrixCelSet:
append, as, as.AffymetrixCelSet, as.character, averageQuantile, byName, byPath, clone, convertToUnique, doCRMAv1, doCRMAv2, doFIRMA, doGCRMA, doRMA, extractAffyBatch, extractFeatureSet, extractMatrix, extractSnpFeatureSet, findByName, getAverage, getAverageAsinh, getAverageFile, getAverageLog, getCdf, getChipType, getData, getIntensities, getPlatform, getTimestamps, getUnitGroupCellMap, getUnitIntensities, getUnitNamesFile, getUnitTypesFile, isDuplicated, justRMA, justSNPRMA, nbrOfArrays, normalizeQuantile, plotDensity, range, readUnits, setCdf, update2, writeSgr
Methods inherited from AffymetrixFileSet:
as, as.AffymetrixFileSet, byPath, getDefaultFullName
Methods inherited from AromaPlatformInterface:
getAromaPlatform, getAromaUflFile, getAromaUgpFile, getChipType, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith
Methods inherited from AromaMicroarrayDataSet:
as.AromaMicroarrayDataSetList, as.AromaMicroarrayDataSetTuple, getAromaFullNameTranslatorSet, getAverageFile, getChipType, getDefaultFullName, getPlatform, setAttributesBy, setAttributesBySampleAnnotationFile, setAttributesBySampleAnnotationSet, validate
Methods inherited from GenericDataFileSet:
[, [[, anyDuplicated, anyNA, append, appendFiles, appendFullNamesTranslator, appendFullNamesTranslatorByNULL, appendFullNamesTranslatorByTabularTextFile, appendFullNamesTranslatorByTabularTextFileSet, appendFullNamesTranslatorBydata.frame, appendFullNamesTranslatorByfunction, appendFullNamesTranslatorBylist, as.character, as.list, byName, byPath, c, clearCache, clearFullNamesTranslator, clone, copyTo, dsApplyInPairs, duplicated, equals, extract, findByName, findDuplicated, getChecksum, getChecksumFileSet, getChecksumObjects, getDefaultFullName, getFile, getFileClass, getFileSize, getFiles, getFullNames, getNames, getOneFile, getPath, getPathnames, getSubdirs, gunzip, gzip, hasFile, indexOf, is.na, names, nbrOfFiles, rep, resetFullNames, setFullNamesTranslator, sortBy, unique, update2, updateFullName, updateFullNames, validate, getFullNameTranslatorSet, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Ken Simpson, Henrik Bengtsson
An object of this class is typically obtained through the
getResidualSet()
method for the ProbeLevelModel
class.
Package: aroma.affymetrix
Class RmaBackgroundCorrection
Object
~~|
~~+--
ParametersInterface
~~~~~~~|
~~~~~~~+--
AromaTransform
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
Transform
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
ProbeLevelTransform
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
BackgroundCorrection
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
RmaBackgroundCorrection
Directly known subclasses:
public static class RmaBackgroundCorrection
extends BackgroundCorrection
This class represents the RMA background adjustment function.
RmaBackgroundCorrection(..., addJitter=FALSE, jitterSd=0.2, seed=6022007)
RmaBackgroundCorrection(..., addJitter=FALSE, jitterSd=0.2, seed=6022007)
... |
Arguments passed to the constructor of
|
addJitter |
If |
jitterSd |
Standard deviation of the jitter noise added. |
seed |
An (optional) |
Internally bg.adjust
is used to background correct the
probe signals. The default is to background correct PM signals only.
Methods:
process |
- | |
Methods inherited from BackgroundCorrection:
getParameters, process
Methods inherited from ProbeLevelTransform:
getRootPath
Methods inherited from Transform:
getOutputDataSet, getOutputFiles
Methods inherited from AromaTransform:
as.character, findFilesTodo, getAsteriskTags, getExpectedOutputFiles, getExpectedOutputFullnames, getFullName, getInputDataSet, getName, getOutputDataSet, getOutputDataSet0, getOutputFiles, getPath, getRootPath, getTags, isDone, process, setTags
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
The fitting algorithm of the RMA background correction model may not converge if there too many small and discrete signals. To overcome this problem, a small amount of noise may be added to the signals before fitting the model. This is an ad hoc solution that seems to work. However, add Gaussian noise may generate non-positive signals.
Ken Simpson, Henrik Bengtsson
Package: aroma.affymetrix
Class RmaCnPlm
Object
~~|
~~+--
ParametersInterface
~~~~~~~|
~~~~~~~+--
Model
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
UnitModel
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
MultiArrayUnitModel
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
ProbeLevelModel
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
RmaPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
RmaSnpPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
SnpPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
CnPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
RmaCnPlm
Directly known subclasses:
public abstract static class RmaCnPlm
extends CnPlm
RmaCnPlm(..., combineAlleles=FALSE)
RmaCnPlm(..., combineAlleles=FALSE)
... |
Arguments passed to |
combineAlleles |
If |
Methods:
No methods defined.
Methods inherited from CnPlm:
getCellIndices, getChipEffectSet, getCombineAlleles, getParameters, getProbeAffinityFile, setCombineAlleles
Methods inherited from SnpPlm:
getCellIndices, getChipEffectSet, getMergeStrands, getParameters, getProbeAffinityFile, setMergeStrands
Methods inherited from RmaSnpPlm:
getAsteriskTags
Methods inherited from RmaPlm:
getAsteriskTags, getCalculateResidualsFunction, getParameters, getRlmFitFunctions
Methods inherited from ProbeLevelModel:
calculateResidualSet, calculateWeights, fit, getAsteriskTags, getCalculateResidualsFunction, getChipEffectSet, getProbeAffinityFile, getResidualSet, getRootPath, getWeightsSet
Methods inherited from MultiArrayUnitModel:
getListOfPriors, setListOfPriors, validate
Methods inherited from UnitModel:
findUnitsTodo, getAsteriskTags, getFitSingleCellUnitFunction, getParameters
Methods inherited from Model:
as.character, fit, getAlias, getAsteriskTags, getDataSet, getFullName, getName, getPath, getRootPath, getTags, setAlias, setTags
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
TO DO.
Henrik Bengtsson
Package: aroma.affymetrix
Class RmaPlm
Object
~~|
~~+--
ParametersInterface
~~~~~~~|
~~~~~~~+--
Model
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
UnitModel
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
MultiArrayUnitModel
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
ProbeLevelModel
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
RmaPlm
Directly known subclasses:
ExonRmaPlm, HetLogAddCnPlm, HetLogAddPlm, HetLogAddSnpPlm, RmaCnPlm, RmaSnpPlm
public abstract static class RmaPlm
extends ProbeLevelModel
This class represents the log-additive model part of the Robust Multichip Analysis (RMA) method described in Irizarry et al (2003).
RmaPlm(..., flavor=c("affyPLM", "oligo"))
RmaPlm(..., flavor=c("affyPLM", "oligo"))
... |
Arguments passed to |
flavor |
A |
Methods:
No methods defined.
Methods inherited from ProbeLevelModel:
calculateResidualSet, calculateWeights, fit, getAsteriskTags, getCalculateResidualsFunction, getChipEffectSet, getProbeAffinityFile, getResidualSet, getRootPath, getWeightsSet
Methods inherited from MultiArrayUnitModel:
getListOfPriors, setListOfPriors, validate
Methods inherited from UnitModel:
findUnitsTodo, getAsteriskTags, getFitSingleCellUnitFunction, getParameters
Methods inherited from Model:
as.character, fit, getAlias, getAsteriskTags, getDataSet, getFullName, getName, getPath, getRootPath, getTags, setAlias, setTags
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
For a single unit group, the log-additive model of RMA is:
where are the chip effects for arrays
,
and
are the probe affinities for probes
.
The
are zero-mean noise with equal variance.
The model is constrained such that
.
Note that all PLM classes must return parameters on the intensity scale.
For this class that means that and
are returned.
There are a few differ algorithms available for fitting the same
probe-level model. The default and recommended method
(flavor="affyPLM"
) uses the implementation in the
preprocessCore package which fits the model parameters robustly
using an M-estimator (the method used to be in affyPLM).
Alternatively, other model-fitting algorithms are available.
The algorithm (flavor="oligo"
) used by the oligo package,
which originates from the affy packages, fits the model using
median polish, which is a non-robust estimator. Note that this algorithm
does not constraint the probe-effect parameters to multiply to one on
the intensity scale. Since the internal function does not return these
estimates, we can neither rescale them.
Henrik Bengtsson, Ken Simpson
Irizarry et al. Summaries of Affymetrix GeneChip probe level data.
NAR, 2003, 31, e15.
Package: aroma.affymetrix
Class RmaSnpPlm
Object
~~|
~~+--
ParametersInterface
~~~~~~~|
~~~~~~~+--
Model
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
UnitModel
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
MultiArrayUnitModel
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
ProbeLevelModel
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
RmaPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
SnpPlm
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
RmaSnpPlm
Directly known subclasses:
RmaCnPlm
public abstract static class RmaSnpPlm
extends SnpPlm
RmaSnpPlm(..., mergeStrands=FALSE)
RmaSnpPlm(..., mergeStrands=FALSE)
... |
Arguments passed to |
mergeStrands |
If |
Methods:
No methods defined.
Methods inherited from SnpPlm:
getCellIndices, getChipEffectSet, getMergeStrands, getParameters, getProbeAffinityFile, setMergeStrands
Methods inherited from RmaPlm:
getAsteriskTags, getCalculateResidualsFunction, getParameters, getRlmFitFunctions
Methods inherited from ProbeLevelModel:
calculateResidualSet, calculateWeights, fit, getAsteriskTags, getCalculateResidualsFunction, getChipEffectSet, getProbeAffinityFile, getResidualSet, getRootPath, getWeightsSet
Methods inherited from MultiArrayUnitModel:
getListOfPriors, setListOfPriors, validate
Methods inherited from UnitModel:
findUnitsTodo, getAsteriskTags, getFitSingleCellUnitFunction, getParameters
Methods inherited from Model:
as.character, fit, getAlias, getAsteriskTags, getDataSet, getFullName, getName, getPath, getRootPath, getTags, setAlias, setTags
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.affymetrix
Class ScaleNormalization
Object
~~|
~~+--
ParametersInterface
~~~~~~~|
~~~~~~~+--
AromaTransform
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
Transform
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
ProbeLevelTransform
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
ScaleNormalization
Directly known subclasses:
public static class ScaleNormalization
extends ProbeLevelTransform
This class represents a normalization function that transforms the probe-level signals towards the same scale.
ScaleNormalization(dataSet=NULL, ..., targetAvg=4400, subsetToUpdate=NULL, typesToUpdate=NULL, subsetToAvg="-XY", typesToAvg=typesToUpdate, shift=0)
ScaleNormalization(dataSet=NULL, ..., targetAvg=4400, subsetToUpdate=NULL, typesToUpdate=NULL, subsetToAvg="-XY", typesToAvg=typesToUpdate, shift=0)
dataSet |
|
... |
Arguments passed to the constructor of
|
targetAvg |
A |
subsetToUpdate |
The probes to be updated.
If |
typesToUpdate |
Types of probes to be updated. |
subsetToAvg |
The probes to calculate average signal over.
If a single |
typesToAvg |
Types of probes to be used when calculating the
average signal.
If |
shift |
Optional amount of shift if data before fitting/normalizing. |
Methods:
process |
- | |
Methods inherited from ProbeLevelTransform:
getRootPath
Methods inherited from Transform:
getOutputDataSet, getOutputFiles
Methods inherited from AromaTransform:
as.character, findFilesTodo, getAsteriskTags, getExpectedOutputFiles, getExpectedOutputFullnames, getFullName, getInputDataSet, getName, getOutputDataSet, getOutputDataSet0, getOutputFiles, getPath, getRootPath, getTags, isDone, process, setTags
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.affymetrix
Class ScaleNormalization3
Object
~~|
~~+--
ParametersInterface
~~~~~~~|
~~~~~~~+--
AromaTransform
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
Transform
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
ProbeLevelTransform
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
ProbeLevelTransform3
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
ScaleNormalization3
Directly known subclasses:
public static class ScaleNormalization3
extends ProbeLevelTransform3
This class represents a normalization function that transforms the probe-level signals towards the same scale.
ScaleNormalization3(..., targetAvg=4400)
ScaleNormalization3(..., targetAvg=4400)
... |
Arguments passed to the constructor of
|
targetAvg |
A |
Methods:
process |
- | |
Methods inherited from ProbeLevelTransform3:
getAsteriskTags, getCellsTo, getCellsToFit, getCellsToUpdate, getParameters, getUnitsTo, getUnitsToFit, getUnitsToUpdate, writeSignals
Methods inherited from ProbeLevelTransform:
getRootPath
Methods inherited from Transform:
getOutputDataSet, getOutputFiles
Methods inherited from AromaTransform:
as.character, findFilesTodo, getAsteriskTags, getExpectedOutputFiles, getExpectedOutputFullnames, getFullName, getInputDataSet, getName, getOutputDataSet, getOutputDataSet0, getOutputFiles, getPath, getRootPath, getTags, isDone, process, setTags
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.affymetrix
Class SingleArrayUnitModel
Object
~~|
~~+--
ParametersInterface
~~~~~~~|
~~~~~~~+--
Model
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
UnitModel
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
SingleArrayUnitModel
Directly known subclasses:
public abstract static class SingleArrayUnitModel
extends UnitModel
This abstract class represents a unit model that fits one model per unit based on signals from a single arrays. The nature of a single-array unit model is that each array can be fitted independently of the others.
SingleArrayUnitModel(...)
SingleArrayUnitModel(...)
... |
Arguments passed to |
Methods:
fit |
- | |
Methods inherited from UnitModel:
findUnitsTodo, getAsteriskTags, getFitSingleCellUnitFunction, getParameters
Methods inherited from Model:
as.character, fit, getAlias, getAsteriskTags, getDataSet, getFullName, getName, getPath, getRootPath, getTags, setAlias, setTags
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.affymetrix
Class SmoothMultiarrayModel
Object
~~|
~~+--
ChromosomalModel
~~~~~~~|
~~~~~~~+--
SmoothMultiarrayModel
Directly known subclasses:
SmoothRmaModel, SmoothSaModel
public abstract static class SmoothMultiarrayModel
extends ChromosomalModel
This abstract class represents a chromosomal smoothing method done chromosome by chromosome.
SmoothMultiarrayModel(..., typoOfWeights=c("none", "1/s2"), bandwidth=10000, tags="*")
SmoothMultiarrayModel(..., typoOfWeights=c("none", "1/s2"), bandwidth=10000, tags="*")
... |
Arguments passed to the constructor of |
typoOfWeights |
A |
bandwidth |
A single |
tags |
Methods:
getBandwidth |
- | |
getOutputTuple |
- | |
setBandwidth |
- | |
Methods inherited from ChromosomalModel:
as.character, fit, getAlias, getAromaGenomeTextFile, getAsteriskTags, getChipType, getChipTypes, getChromosomes, getFullName, getFullNames, getGenome, getGenomeData, getGenomeFile, getListOfAromaUgpFiles, getName, getNames, getParentPath, getPath, getReportPath, getRootPath, getSetTuple, getSets, getTags, indexOf, nbrOfArrays, nbrOfChipTypes, setChromosomes, setGenome, getListOfGenomeInformations, getPcuTheta, getPositionChipTypeUnit
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.affymetrix
Class SmoothRmaModel
Object
~~|
~~+--
ChromosomalModel
~~~~~~~|
~~~~~~~+--
SmoothMultiarrayModel
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
SmoothRmaModel
Directly known subclasses:
public abstract static class SmoothRmaModel
extends SmoothMultiarrayModel
This class represents the Chromosomal Smoothing Robust Multichip Analysis method.
SmoothRmaModel(...)
SmoothRmaModel(...)
... |
Arguments passed to the constructor of
|
Methods:
No methods defined.
Methods inherited from SmoothMultiarrayModel:
as.character, createOutputTuple, fitOneChromosome, getAsteriskTags, getBandwidth, getFitUnitGroupFunction, getOutputTuple, getRootPath, setBandwidth
Methods inherited from ChromosomalModel:
as.character, fit, getAlias, getAromaGenomeTextFile, getAsteriskTags, getChipType, getChipTypes, getChromosomes, getFullName, getFullNames, getGenome, getGenomeData, getGenomeFile, getListOfAromaUgpFiles, getName, getNames, getParentPath, getPath, getReportPath, getRootPath, getSetTuple, getSets, getTags, indexOf, nbrOfArrays, nbrOfChipTypes, setChromosomes, setGenome, getListOfGenomeInformations, getPcuTheta, getPositionChipTypeUnit
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.affymetrix
Class SnpChipEffectFile
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
CacheKeyInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
AromaMicroarrayDataFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixCelFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
ParametersInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
ParameterCelFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
ChipEffectFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
SnpChipEffectFile
Directly known subclasses:
CnChipEffectFile
public abstract static class SnpChipEffectFile
extends ChipEffectFile
This class represents estimates of chip effects in the probe-level models.
SnpChipEffectFile(..., mergeStrands=FALSE)
SnpChipEffectFile(..., mergeStrands=FALSE)
... |
Arguments passed to |
mergeStrands |
Specifies if the strands are merged or not for these estimates. |
Methods:
extractTheta |
- | |
extractTotalAndFracB |
- | |
readUnits |
- | |
Methods inherited from ChipEffectFile:
as.character, extractChromosomalDataFrame, extractMatrix, extractTheta, findUnitsTodo, getAM, getAsFullCelFile, getCellIndices, getCellMapForMainCdf, getExpandedCellMap, getParameters, getUnitGroupCellArrayMap, getUnitGroupCellMatrixMap, getXAM, mergeGroups, readUnits, writeAsFullCelFile
Methods inherited from ParameterCelFile:
extractDataFrame, extractMatrix, readUnits
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from AffymetrixCelFile:
allocateFromCdf, as.character, clone, createFrom, extractMatrix, fromFile, getAm, getCdf, getExtensionPattern, getFileFormat, getImage, getUnitNamesFile, getUnitTypesFile, highlight, image270, nbrOfCells, plotDensity, plotImage, plotMvsA, plotMvsX, range, setCdf, smoothScatterMvsA, writeImage
Methods inherited from AromaPlatformInterface:
getAromaPlatform, getAromaUflFile, getAromaUgpFile, getChipType, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith
Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags
Methods inherited from FileCacheKeyInterface:
getCacheKey
Methods inherited from CacheKeyInterface:
getCacheKey
Methods inherited from GenericDataFile:
as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
An object of this class is typically part of a SnpChipEffectSet
.
Package: aroma.affymetrix
Class SnpChipEffectSet
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFileSet
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
AromaMicroarrayDataSet
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixFileSet
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixCelSet
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
ParametersInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
ParameterCelSet
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
ChipEffectSet
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
SnpChipEffectSet
Directly known subclasses:
CnChipEffectSet
public static class SnpChipEffectSet
extends ChipEffectSet
This class represents estimates of chip effects in the probe-level models.
SnpChipEffectSet(..., mergeStrands="byFirstFile")
SnpChipEffectSet(..., mergeStrands="byFirstFile")
... |
Arguments passed to |
mergeStrands |
Specifies if the strands are merged or not for these estimates. |
Methods:
extractAlleleSet |
- | |
extractSnpCnvQSet |
- | |
extractSnpQSet |
- | |
extractTheta |
- | |
extractTotalAndFreqB |
- | |
getAverageFile |
- | |
getMergeStrands |
- | |
setMergeStrands |
- | |
Methods inherited from ChipEffectSet:
as.character, boxplotStats, byPath, calculateBaseline, calculateFieldBoxplotStats, calculateNuseBoxplotStats, calculateRleBoxplotStats, extractAffyBatch, extractChromosomalDataFrame, extractExpressionSet, extractMatrix, extractTheta, findByName, findUnitsTodo, fromDataSet, getAM, getAsFullCelSet, getAverageFile, getBaseline, getCellIndices, getXAM, plotBoxplot, readUnits, updateUnits
Methods inherited from ParameterCelSet:
extractDataFrame, extractMatrix
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from AffymetrixCelSet:
append, as, as.AffymetrixCelSet, as.character, averageQuantile, byName, byPath, clone, convertToUnique, doCRMAv1, doCRMAv2, doFIRMA, doGCRMA, doRMA, extractAffyBatch, extractFeatureSet, extractMatrix, extractSnpFeatureSet, findByName, getAverage, getAverageAsinh, getAverageFile, getAverageLog, getCdf, getChipType, getData, getIntensities, getPlatform, getTimestamps, getUnitGroupCellMap, getUnitIntensities, getUnitNamesFile, getUnitTypesFile, isDuplicated, justRMA, justSNPRMA, nbrOfArrays, normalizeQuantile, plotDensity, range, readUnits, setCdf, update2, writeSgr
Methods inherited from AffymetrixFileSet:
as, as.AffymetrixFileSet, byPath, getDefaultFullName
Methods inherited from AromaPlatformInterface:
getAromaPlatform, getAromaUflFile, getAromaUgpFile, getChipType, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith
Methods inherited from AromaMicroarrayDataSet:
as.AromaMicroarrayDataSetList, as.AromaMicroarrayDataSetTuple, getAromaFullNameTranslatorSet, getAverageFile, getChipType, getDefaultFullName, getPlatform, setAttributesBy, setAttributesBySampleAnnotationFile, setAttributesBySampleAnnotationSet, validate
Methods inherited from GenericDataFileSet:
[, [[, anyDuplicated, anyNA, append, appendFiles, appendFullNamesTranslator, appendFullNamesTranslatorByNULL, appendFullNamesTranslatorByTabularTextFile, appendFullNamesTranslatorByTabularTextFileSet, appendFullNamesTranslatorBydata.frame, appendFullNamesTranslatorByfunction, appendFullNamesTranslatorBylist, as.character, as.list, byName, byPath, c, clearCache, clearFullNamesTranslator, clone, copyTo, dsApplyInPairs, duplicated, equals, extract, findByName, findDuplicated, getChecksum, getChecksumFileSet, getChecksumObjects, getDefaultFullName, getFile, getFileClass, getFileSize, getFiles, getFullNames, getNames, getOneFile, getPath, getPathnames, getSubdirs, gunzip, gzip, hasFile, indexOf, is.na, names, nbrOfFiles, rep, resetFullNames, setFullNamesTranslator, sortBy, unique, update2, updateFullName, updateFullNames, validate, getFullNameTranslatorSet, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.affymetrix
Class SnpInformation
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
CacheKeyInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
SnpInformation
Directly known subclasses:
DChipSnpInformation, UflSnpInformation
public abstract static class SnpInformation
extends FileCacheKeyInterface
SnpInformation(...)
SnpInformation(...)
... |
Arguments passed to |
Methods:
byChipType |
- | |
getChipType |
- | |
getData |
- | |
getFragmentLengths |
- | |
getFragmentStarts |
- | |
getFragmentStops |
- | |
nbrOfEnzymes |
- | |
nbrOfUnits |
- | |
readDataFrame |
- | |
Methods inherited from FileCacheKeyInterface:
getCacheKey
Methods inherited from CacheKeyInterface:
getCacheKey
Methods inherited from GenericDataFile:
as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.affymetrix
Class SnpPlm
Interface
~~|
~~+--
SnpPlm
Directly known subclasses:
AffineCnPlm, AffineSnpPlm, AvgCnPlm, AvgSnpPlm, CnPlm, HetLogAddCnPlm, HetLogAddSnpPlm, MbeiCnPlm, MbeiSnpPlm, RmaCnPlm, RmaSnpPlm
public class SnpPlm
extends Interface
An Interface
implementing methods special for
ProbeLevelModel
s specific to SNP arrays.
SnpPlm(...)
SnpPlm(...)
... |
Not used. |
Methods:
getCellIndices |
- | |
getChipEffectSet |
- | |
getMergeStrands |
- | |
getProbeAffinityFile |
- | |
setMergeStrands |
- | |
Methods inherited from Interface:
extend, print, uses
Classes inheriting from this Interface
must provide the
following fields:
A logical
value indicating if strands should be
merged or not.
Henrik Bengtsson
for (zzz in 0) { # Setup verbose output verbose <- Arguments$getVerbose(-2) timestampOn(verbose) # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Define an example dataset using this path # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Find any SNP dataset path <- NULL if (is.null(path)) break if (!exists("ds")) { ds <- AffymetrixCelSet$fromFiles(path) } print(ds) # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Create a set of various PLMs for this dataset # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - if (!exists("models", mode="list")) { mergeStrands <- TRUE models <- list( rma = RmaSnpPlm(ds, mergeStrands=mergeStrands), mbei = MbeiSnpPlm(ds, mergeStrands=mergeStrands) # affine = AffineSnpPlm(ds, background=FALSE, mergeStrands=mergeStrands) ) } print(models) # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # For each model, fit a few units # # Note, by fitting the same set of units across models, the internal # caching mechanisms of aroma.affymetrix makes sure that the data is # only read into memory once. See log for reading speed. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - units <- 55+1:100 for (model in models) { ruler(verbose) fit(model, units=units, force=TRUE, verbose=verbose) } # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # For each unit, plot the estimated (thetaB,thetaA) for all models # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Should we plot the on the log scale? log <- TRUE # Do only user to press ENTER if more than one unit is plotted opar <- par(ask=(length(units) > 1)) Alab <- expression(theta[A]) Blab <- expression(theta[B]) if (log) { lim <- c(6, 16) } else { lim <- c(0, 2^15) } # For each unit... for (unit in units) { # For all models... for (kk in seq_along(models)) { ces <- getChipEffects(models[[kk]]) ceUnit <- ces[unit] snpName <- names(ceUnit)[1] theta <- ceUnit[[1]] thetaA <- theta[[1]]$theta thetaB <- theta[[2]]$theta if (log) { thetaA <- log(thetaA, base=2) thetaB <- log(thetaB, base=2) } # Create the plot? if (kk == 1) { plot(NA, xlim=lim, ylim=lim, xlab=Blab, ylab=Alab, main=snpName) abline(a=0, b=1, lty=2) } # Plot the estimated parameters points(thetaB, thetaA, col=kk, pch=19) } } # for (unit ...) # Reset graphical parameter settings par(opar) } # for (zzz in 0) rm(zzz)
for (zzz in 0) { # Setup verbose output verbose <- Arguments$getVerbose(-2) timestampOn(verbose) # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Define an example dataset using this path # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Find any SNP dataset path <- NULL if (is.null(path)) break if (!exists("ds")) { ds <- AffymetrixCelSet$fromFiles(path) } print(ds) # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Create a set of various PLMs for this dataset # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - if (!exists("models", mode="list")) { mergeStrands <- TRUE models <- list( rma = RmaSnpPlm(ds, mergeStrands=mergeStrands), mbei = MbeiSnpPlm(ds, mergeStrands=mergeStrands) # affine = AffineSnpPlm(ds, background=FALSE, mergeStrands=mergeStrands) ) } print(models) # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # For each model, fit a few units # # Note, by fitting the same set of units across models, the internal # caching mechanisms of aroma.affymetrix makes sure that the data is # only read into memory once. See log for reading speed. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - units <- 55+1:100 for (model in models) { ruler(verbose) fit(model, units=units, force=TRUE, verbose=verbose) } # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # For each unit, plot the estimated (thetaB,thetaA) for all models # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Should we plot the on the log scale? log <- TRUE # Do only user to press ENTER if more than one unit is plotted opar <- par(ask=(length(units) > 1)) Alab <- expression(theta[A]) Blab <- expression(theta[B]) if (log) { lim <- c(6, 16) } else { lim <- c(0, 2^15) } # For each unit... for (unit in units) { # For all models... for (kk in seq_along(models)) { ces <- getChipEffects(models[[kk]]) ceUnit <- ces[unit] snpName <- names(ceUnit)[1] theta <- ceUnit[[1]] thetaA <- theta[[1]]$theta thetaB <- theta[[2]]$theta if (log) { thetaA <- log(thetaA, base=2) thetaB <- log(thetaB, base=2) } # Create the plot? if (kk == 1) { plot(NA, xlim=lim, ylim=lim, xlab=Blab, ylab=Alab, main=snpName) abline(a=0, b=1, lty=2) } # Plot the estimated parameters points(thetaB, thetaA, col=kk, pch=19) } } # for (unit ...) # Reset graphical parameter settings par(opar) } # for (zzz in 0) rm(zzz)
Package: aroma.affymetrix
Class SnpProbeAffinityFile
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
CacheKeyInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
AromaMicroarrayDataFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixCelFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
ParametersInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
ParameterCelFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
ProbeAffinityFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
SnpProbeAffinityFile
Directly known subclasses:
CnProbeAffinityFile
public abstract static class SnpProbeAffinityFile
extends ProbeAffinityFile
This class represents estimates of probe affinities in SNP probe-level models.
SnpProbeAffinityFile(..., mergeStrands=FALSE)
SnpProbeAffinityFile(..., mergeStrands=FALSE)
... |
Arguments passed to |
mergeStrands |
Specifies if the strands are merged or not for these estimates. |
Methods:
No methods defined.
Methods inherited from ProbeAffinityFile:
as.character, getCellIndices, getParameters, readUnits
Methods inherited from ParameterCelFile:
extractDataFrame, extractMatrix, readUnits
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from AffymetrixCelFile:
allocateFromCdf, as.character, clone, createFrom, extractMatrix, fromFile, getAm, getCdf, getExtensionPattern, getFileFormat, getImage, getUnitNamesFile, getUnitTypesFile, highlight, image270, nbrOfCells, plotDensity, plotImage, plotMvsA, plotMvsX, range, setCdf, smoothScatterMvsA, writeImage
Methods inherited from AromaPlatformInterface:
getAromaPlatform, getAromaUflFile, getAromaUgpFile, getChipType, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith
Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags
Methods inherited from FileCacheKeyInterface:
getCacheKey
Methods inherited from CacheKeyInterface:
getCacheKey
Methods inherited from GenericDataFile:
as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.affymetrix
Class SpatialReporter
Object
~~|
~~+--
GenericReporter
~~~~~~~|
~~~~~~~+--
AffymetrixFileSetReporter
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
AffymetrixCelSetReporter
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
SpatialReporter
Directly known subclasses:
public abstract static class SpatialReporter
extends AffymetrixCelSetReporter
A SpatialReporter generates image files of spatial representations of cell signals for each of the arrays in the input set.
SpatialReporter(..., reference=NULL)
SpatialReporter(..., reference=NULL)
... |
Arguments passed to |
reference |
An optional reference |
Methods:
addColorMap |
- | |
getColorMaps |
- | |
plotMargins |
- | |
process |
- | |
setColorMaps |
- | |
Methods inherited from AffymetrixCelSetReporter:
as.character, getChipType, getDataSet, getPath, nbrOfArrays
Methods inherited from AffymetrixFileSetReporter:
getFileSet, getInputName, getInputTags
Methods inherited from GenericReporter:
as.character, getAlias, getAsteriskTags, getFullName, getInputName, getInputTags, getMainPath, getName, getPath, getReportSet, getRootPath, getTags, process, setAlias, setup
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.affymetrix
Class TransformReport
Object
~~|
~~+--
TransformReport
Directly known subclasses:
public static class TransformReport
extends Object
TransformReport(inSet=NULL, outSet=NULL, ...)
TransformReport(inSet=NULL, outSet=NULL, ...)
inSet |
The input data set as an |
outSet |
The output data set as an |
... |
Not used. |
Methods:
getCdf |
- | |
getFullName |
- | |
getInputDataSet |
- | |
getName |
- | |
getOutputDataSet |
- | |
getPath |
- | |
getTags |
- | |
getUnitNamesFile |
- | |
getUnitTypesFile |
- | |
getYY |
- | |
nbrOfArrays |
- | |
plotXYCurve |
- | |
plotXYCurveLog2 |
- | |
seq |
- | |
writeImageCombined |
- | |
writeImages |
- | |
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.affymetrix
Class UgpGenomeInformation
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
CacheKeyInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
GenomeInformation
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
UgpGenomeInformation
Directly known subclasses:
public abstract static class UgpGenomeInformation
extends GenomeInformation
This class represents Aroma UGP genome information files.
UgpGenomeInformation(..., .ugp=NULL, .verify=TRUE)
UgpGenomeInformation(..., .ugp=NULL, .verify=TRUE)
... |
Arguments passed to |
.ugp |
For internal use only. |
.verify |
For internal use only. |
Methods:
byChipType |
- | |
getChipType |
- | |
getChromosomes |
- | |
getData |
- | |
getUnitsOnChromosome |
- | |
isCompatibleWithCdf |
- | |
nbrOfUnits |
- | |
readDataFrame |
- | |
Methods inherited from GenomeInformation:
as.character, byChipType, fromCdf, fromDataSet, getChipType, getChromosomeStats, getChromosomes, getData, getPositions, getUnitIndices, getUnitsOnChromosome, getUnitsOnChromosomes, isCompatibleWithCdf, nbrOfUnits, plotDensity, readDataFrame, verify
Methods inherited from FileCacheKeyInterface:
getCacheKey
Methods inherited from CacheKeyInterface:
getCacheKey
Methods inherited from GenericDataFile:
as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.affymetrix
Class UnitModel
Object
~~|
~~+--
ParametersInterface
~~~~~~~|
~~~~~~~+--
Model
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
UnitModel
Directly known subclasses:
AffineCnPlm, AffinePlm, AffineSnpPlm, AlleleSummation, AvgCnPlm, AvgPlm, AvgSnpPlm, ExonRmaPlm, FirmaModel, HetLogAddCnPlm, HetLogAddPlm, HetLogAddSnpPlm, MbeiCnPlm, MbeiPlm, MbeiSnpPlm, MultiArrayUnitModel, ProbeLevelModel, RmaCnPlm, RmaPlm, RmaSnpPlm, SingleArrayUnitModel
public abstract static class UnitModel
extends Model
This class is abstract and represents a generic unit model, i.e. a model that is applied to each unit separately.
UnitModel(dataSet=NULL, probeModel=c("pm", "mm", "pm-mm", "min1(pm-mm)", "pm+mm"), shift=0, ...)
UnitModel(dataSet=NULL, probeModel=c("pm", "mm", "pm-mm", "min1(pm-mm)", "pm+mm"), shift=0, ...)
dataSet |
An |
probeModel |
A |
shift |
An optional amount the signals should be shifted (translated) before fitting the model. |
... |
Arguments passed to the constructor of |
Methods:
findUnitsTodo |
- | |
Methods inherited from Model:
as.character, fit, getAlias, getAsteriskTags, getDataSet, getFullName, getName, getPath, getRootPath, getTags, setAlias, setTags
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.affymetrix
Class UnitTypeScaleNormalization
Object
~~|
~~+--
ParametersInterface
~~~~~~~|
~~~~~~~+--
AromaTransform
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
Transform
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
ProbeLevelTransform
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
ProbeLevelTransform3
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
UnitTypeScaleNormalization
Directly known subclasses:
public static class UnitTypeScaleNormalization
extends ProbeLevelTransform3
This class represents a normalization function that transforms the probe signals such that each unit type gets the same average.
UnitTypeScaleNormalization(..., targetAvg=4400)
UnitTypeScaleNormalization(..., targetAvg=4400)
... |
Arguments passed to the constructor of
|
targetAvg |
A |
Methods:
process |
- | |
Methods inherited from ProbeLevelTransform3:
getAsteriskTags, getCellsTo, getCellsToFit, getCellsToUpdate, getParameters, getUnitsTo, getUnitsToFit, getUnitsToUpdate, writeSignals
Methods inherited from ProbeLevelTransform:
getRootPath
Methods inherited from Transform:
getOutputDataSet, getOutputFiles
Methods inherited from AromaTransform:
as.character, findFilesTodo, getAsteriskTags, getExpectedOutputFiles, getExpectedOutputFullnames, getFullName, getInputDataSet, getName, getOutputDataSet, getOutputDataSet0, getOutputFiles, getPath, getRootPath, getTags, isDone, process, setTags
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.affymetrix
Class WeightsFile
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
CacheKeyInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
AromaMicroarrayDataFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixCelFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
ParametersInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
ParameterCelFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
WeightsFile
Directly known subclasses:
public abstract static class WeightsFile
extends ParameterCelFile
This class represents weights calculated from residuals of probe-level models.
WeightsFile(..., probeModel=c("pm"))
WeightsFile(..., probeModel=c("pm"))
... |
Arguments passed to |
probeModel |
The specific type of model, e.g. |
Methods:
findUnitsTodo |
- | |
getImage |
- | |
readUnits |
- | |
writeImage |
- | |
Methods inherited from ParameterCelFile:
extractDataFrame, extractMatrix, readUnits
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from AffymetrixCelFile:
allocateFromCdf, as.character, clone, createFrom, extractMatrix, fromFile, getAm, getCdf, getExtensionPattern, getFileFormat, getImage, getUnitNamesFile, getUnitTypesFile, highlight, image270, nbrOfCells, plotDensity, plotImage, plotMvsA, plotMvsX, range, setCdf, smoothScatterMvsA, writeImage
Methods inherited from AromaPlatformInterface:
getAromaPlatform, getAromaUflFile, getAromaUgpFile, getChipType, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith
Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags
Methods inherited from FileCacheKeyInterface:
getCacheKey
Methods inherited from CacheKeyInterface:
getCacheKey
Methods inherited from GenericDataFile:
as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson, Ken Simpson
An object of this class is typically obtained through the
getWeightsSet()
method for the ProbeLevelModel
class.
An object of this class is typically part of a WeightsSet
.
Package: aroma.affymetrix
Class WeightsSet
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFileSet
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
AromaMicroarrayDataSet
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixFileSet
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AffymetrixCelSet
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
ParametersInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
WeightsSet
Directly known subclasses:
public static class WeightsSet
extends ParametersInterface
This class represents probe-level weights.
WeightsSet(..., probeModel=c("pm"))
WeightsSet(..., probeModel=c("pm"))
... |
Arguments passed to |
probeModel |
The specific type of model, e.g. |
Methods:
findUnitsTodo |
- | |
getAverageFile |
- | |
getCellIndices |
- | |
readUnits |
- | |
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from AffymetrixCelSet:
append, as, as.AffymetrixCelSet, as.character, averageQuantile, byName, byPath, clone, convertToUnique, doCRMAv1, doCRMAv2, doFIRMA, doGCRMA, doRMA, extractAffyBatch, extractFeatureSet, extractMatrix, extractSnpFeatureSet, findByName, getAverage, getAverageAsinh, getAverageFile, getAverageLog, getCdf, getChipType, getData, getIntensities, getPlatform, getTimestamps, getUnitGroupCellMap, getUnitIntensities, getUnitNamesFile, getUnitTypesFile, isDuplicated, justRMA, justSNPRMA, nbrOfArrays, normalizeQuantile, plotDensity, range, readUnits, setCdf, update2, writeSgr
Methods inherited from AffymetrixFileSet:
as, as.AffymetrixFileSet, byPath, getDefaultFullName
Methods inherited from AromaPlatformInterface:
getAromaPlatform, getAromaUflFile, getAromaUgpFile, getChipType, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith
Methods inherited from AromaMicroarrayDataSet:
as.AromaMicroarrayDataSetList, as.AromaMicroarrayDataSetTuple, getAromaFullNameTranslatorSet, getAverageFile, getChipType, getDefaultFullName, getPlatform, setAttributesBy, setAttributesBySampleAnnotationFile, setAttributesBySampleAnnotationSet, validate
Methods inherited from GenericDataFileSet:
[, [[, anyDuplicated, anyNA, append, appendFiles, appendFullNamesTranslator, appendFullNamesTranslatorByNULL, appendFullNamesTranslatorByTabularTextFile, appendFullNamesTranslatorByTabularTextFileSet, appendFullNamesTranslatorBydata.frame, appendFullNamesTranslatorByfunction, appendFullNamesTranslatorBylist, as.character, as.list, byName, byPath, c, clearCache, clearFullNamesTranslator, clone, copyTo, dsApplyInPairs, duplicated, equals, extract, findByName, findDuplicated, getChecksum, getChecksumFileSet, getChecksumObjects, getDefaultFullName, getFile, getFileClass, getFileSize, getFiles, getFullNames, getNames, getOneFile, getPath, getPathnames, getSubdirs, gunzip, gzip, hasFile, indexOf, is.na, names, nbrOfFiles, rep, resetFullNames, setFullNamesTranslator, sortBy, unique, update2, updateFullName, updateFullNames, validate, getFullNameTranslatorSet, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson, Ken Simpson
An object of this class is typically obtained through the
getWeightsSet()
method for the ProbeLevelModel
class.