Package 'aroma.affymetrix' reference manual

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:	2024-07-17 11:21:38 UTC
Source:	https://github.com/HenrikBengtsson/aroma.affymetrix

Package aroma.affymetrix

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.

Installation and updates

The preferred way to install this package is:

   source("https://callr.org/install#aroma.affymetrix")

To get started

To get started, see the online user guides and the vignettes https://www.aroma-project.org/.

How to cite this package

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.

License

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.

Author(s)

Henrik Bengtsson, James Bullard, Kasper Hansen, Pierre Neuvial, Elizabeth Purdom, Mark Robinson, Ken Simpson

References

[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/.

The AbstractProbeSequenceNormalization class

Description

Package: aroma.affymetrix
Class 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.

Usage

AbstractProbeSequenceNormalization(..., target=NULL)
AbstractProbeSequenceNormalization(..., target=NULL)

Arguments

`...`	Arguments passed to the constructor of `ProbeLevelTransform3`.
`target`	A `character` string specifying type of "target" used. If `"zero"`, all arrays are normalized to have no effects. If `NULL`, all arrays a normalized to have the same effect as the average array has.

Fields and Methods

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

Requirements

This class requires that an AromaCellSequenceFile is available for the chip type.

Author(s)

Henrik Bengtsson

The AdditiveCovariatesNormalization class

Description

Package: aroma.affymetrix
Class 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.

Usage

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"))

Arguments

`dataSet`	A `SnpChipEffectSet`.
`...`	Additional arguments passed to the constructor of `ChipEffectTransform`.
`target`	(Optional) A `character` string or a `function` specifying what to normalize toward.
`subsetToFit`	The units from which the normalization curve should be estimated. If `NULL`, all are considered.
`onMissing`	Specifies how to normalize units for which the GC contents are unknown.
`shift`	An optional amount the data points should be shifted (translated).

Details

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.

Fields and Methods

Methods:

	`getCdf`	-
	`process`	-

Methods inherited from ChipEffectTransform:
getRootPath

Methods inherited from Transform:
getOutputDataSet, getOutputFiles

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Author(s)

Henrik Bengtsson

The AffineCnPlm class

Description

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

Usage

AffineCnPlm(..., combineAlleles=FALSE)
AffineCnPlm(..., combineAlleles=FALSE)

Arguments

`...`	Arguments passed to `AffineSnpPlm`.
`combineAlleles`	If `FALSE`, allele A and allele B are treated separately, otherwise together.

Fields and Methods

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

Author(s)

Henrik Bengtsson

The AffinePlm class

Description

Package: aroma.affymetrix
Class AffinePlm

Directly known subclasses:
AffineCnPlm, AffineSnpPlm

public abstract static class AffinePlm
extends ProbeLevelModel

This class represents affine model in Bengtsson & Hossjer (2006).

Usage

AffinePlm(..., background=TRUE)
AffinePlm(..., background=TRUE)

Arguments

`...`	Arguments passed to `ProbeLevelModel`.
`background`	If `TRUE`, background is estimate for each unit group, otherwise not. That is, if `FALSE`, a linear (proportional) model without offset is fitted, resulting in very similar results as obtained by the `MbeiPlm`.

Fields and Methods

Methods:

	`getProbeAffinityFile`	-

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

Model

For a single unit group, the affine model is:

$y_{ik} = a + \theta_i \phi_k + \varepsilon_{ik}$

where $a$ is an offset common to all probe signals, $\theta_i$ are the chip effects for arrays $i=1,...,I$ , and $\phi_k$ are the probe affinities for probes $k=1,...,K$ . The $\varepsilon_{ik}$ are zero-mean noise with equal variance. The model is constrained such that $\prod_k \phi_k = 1$ .

Note that with the additional constraint $a=0$ (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.

Author(s)

Henrik Bengtsson

References

Bengtsson & Hossjer (2006).

The AffineSnpPlm class

Description

Package: aroma.affymetrix
Class AffineSnpPlm

Directly known subclasses:
AffineCnPlm

public abstract static class AffineSnpPlm
extends SnpPlm

Usage

AffineSnpPlm(..., mergeStrands=FALSE)
AffineSnpPlm(..., mergeStrands=FALSE)

Arguments

`...`	Arguments passed to `AffinePlm`.
`mergeStrands`	If `TRUE`, the sense and the anti-sense strands are fitted together, otherwise separately.

Fields and Methods

Methods:
No methods defined.

Methods inherited from SnpPlm:
getCellIndices, getChipEffectSet, getMergeStrands, getParameters, getProbeAffinityFile, setMergeStrands

Methods inherited from AffinePlm:
getAsteriskTags, getFitUnitGroupFunction, getProbeAffinityFile

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

Author(s)

Henrik Bengtsson

The AffymetrixCdfFile class

Description

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.

Usage

AffymetrixCdfFile(...)
AffymetrixCdfFile(...)

Arguments

...

Arguments passed to AromaChipTypeAnnotationFile.

Fields and Methods

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

Author(s)

Henrik Bengtsson, Ken Simpson

The AffymetrixCelFile class

Description

Package: aroma.affymetrix
Class 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.

Usage

AffymetrixCelFile(..., cdf=NULL)
AffymetrixCelFile(..., cdf=NULL)

Arguments

`...`	Arguments passed to `AromaMicroarrayDataFile`.
`cdf`	An optional `AffymetrixCdfFile` making it possible to override the default CDF file as specified by the CEL file header. The requirement is that its number of cells must match that of the CEL file. If `NULL`, the CDF structure is inferred from the the chip type as specified in the CEL file header.

Fields and Methods

Methods:

	`extractMatrix`	-
	`getAm`	-
	`getCdf`	-
	`getFileFormat`	-
	`getImage`	-
	`getUnitNamesFile`	-
	`getUnitTypesFile`	-
	`image270`	-
	`nbrOfCells`	-
	`plotDensity`	-
	`plotImage`	-
	`plotMvsA`	-
	`plotMvsX`	-
	`setCdf`	-
	`smoothScatterMvsA`	-
	`writeImage`	-

Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

For developers

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.

Author(s)

Henrik Bengtsson

The AffymetrixCelSet class

Description

Package: aroma.affymetrix
Class 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.

Usage

AffymetrixCelSet(files=NULL, ...)
AffymetrixCelSet(files=NULL, ...)

Arguments

`files`	A `list` of `AffymetrixCelFile`:s.
`...`	Not used.

Fields and Methods

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 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

Author(s)

Henrik Bengtsson

Examples

## 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)

The AffymetrixCelSetReporter class

Description

Package: aroma.affymetrix
Class AffymetrixCelSetReporter

Object
~~|
~~+--GenericReporter
~~~~~~~|
~~~~~~~+--AffymetrixFileSetReporter
~~~~~~~~~~~~|
~~~~~~~~~~~~+--AffymetrixCelSetReporter

Directly known subclasses:
SpatialReporter

public abstract static class AffymetrixCelSetReporter
extends AffymetrixFileSetReporter

Usage

AffymetrixCelSetReporter(..., .setClass="AffymetrixCelSet")
AffymetrixCelSetReporter(..., .setClass="AffymetrixCelSet")

Arguments

`...`	Arguments passed to `AffymetrixFileSetReporter`.
`.setClass`	The name of the class of the input set.

Fields and Methods

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

Author(s)

Henrik Bengtsson

The AffymetrixCelSetTuple class

Description

Package: aroma.affymetrix
Class AffymetrixCelSetTuple

Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFileSetList
~~~~~~~~~~~~|
~~~~~~~~~~~~+--AromaMicroarrayDataSetTuple
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--AffymetrixCelSetTuple

Directly known subclasses:
ChipEffectSetTuple, CnChipEffectSetTuple

public static class AffymetrixCelSetTuple
extends AromaMicroarrayDataSetTuple

Usage

AffymetrixCelSetTuple(..., .setClass="AffymetrixCelSet")
AffymetrixCelSetTuple(..., .setClass="AffymetrixCelSet")

Arguments

`...`	Arguments passed to the constructor of `AromaMicroarrayDataSetTuple`.
`.setClass`	The name of the class of the input set.

Fields and Methods

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

Author(s)

Henrik Bengtsson

The AffymetrixCnChpSet class

Description

Package: aroma.affymetrix
Class AffymetrixCnChpSet

Directly known subclasses:

public abstract static class AffymetrixCnChpSet
extends AffymetrixFileSet

A AffymetrixCnChpSet object represents a set of AffymetrixCnChpFile:s with identical chip types.

Usage

AffymetrixCnChpSet(files=NULL, ...)
AffymetrixCnChpSet(files=NULL, ...)

Arguments

`files`	A `list` of `AffymetrixCnChpFile`:s.
`...`	Not used.

Fields and Methods

Methods:

	`as`	-
	`as.AffymetrixCnChpSet`	-
	`exportTotalCnRatioSet`	-
	`extractLogRatios`	-
	`findByName`	-
	`getCdf`	-
	`setCdf`	-

Methods inherited from AffymetrixFileSet:
as, as.AffymetrixFileSet, byPath, getDefaultFullName

Author(s)

Henrik Bengtsson

The abstract AffymetrixFile class

Description

Package: aroma.affymetrix
Class 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.

Usage

AffymetrixFile(...)
AffymetrixFile(...)

Arguments

...

Arguments passed to GenericDataFile.

Fields and Methods

Methods:
No methods defined.

Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Author(s)

Henrik Bengtsson

The AffymetrixFileSet class

Description

Package: aroma.affymetrix
Class 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 AffymetrixFiles with identical chip types.

Usage

AffymetrixFileSet(files=NULL, ...)
AffymetrixFileSet(files=NULL, ...)

Arguments

`files`	A `list` of `AffymetrixFile`:s.
`...`	Arguments passed to `GenericDataFileSet`.

Fields and Methods

Methods:

	`as`	-
	`as.AffymetrixFileSet`	-
	`byPath`	-

Author(s)

Henrik Bengtsson

The AffymetrixFileSetReporter class

Description

Package: aroma.affymetrix
Class AffymetrixFileSetReporter

Object
~~|
~~+--GenericReporter
~~~~~~~|
~~~~~~~+--AffymetrixFileSetReporter

Directly known subclasses:
AffymetrixCelSetReporter, SpatialReporter

public abstract static class AffymetrixFileSetReporter
extends GenericReporter

Usage

AffymetrixFileSetReporter(set=NULL, ..., .setClass="AffymetrixFileSet")
AffymetrixFileSetReporter(set=NULL, ..., .setClass="AffymetrixFileSet")

Arguments

`set`	An `AffymetrixFileSet` object.
`...`	Arguments passed to `GenericReporter`.
`.setClass`	The name of the class of the input set.

Fields and Methods

Methods:

	`getInputName`	-
	`getInputTags`	-

Author(s)

Henrik Bengtsson

The AffymetrixPgfFile class

Description

Package: aroma.affymetrix
Class 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]

Usage

AffymetrixPgfFile(...)
AffymetrixPgfFile(...)

Arguments

...

Arguments passed to AromaChipTypeAnnotationFile.

Fields and Methods

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 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

Author(s)

Henrik Bengtsson

References

[1] ...

The AlleleSummation class

Description

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.

Usage

AlleleSummation(dataSet=NULL, ignoreNAs=TRUE, ...)
AlleleSummation(dataSet=NULL, ignoreNAs=TRUE, ...)

Arguments

`dataSet`	A `SnpChipEffectSet`.
`ignoreNAs`	If `TRUE`, missing values are excluded when summing the signals from the two alleles.
`...`	Arguments passed to `UnitModel`.

Fields and Methods

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

Author(s)

Henrik Bengtsson

The AllelicCrosstalkCalibration class

Description

Package: aroma.affymetrix
Class 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.

Usage

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"))

Arguments

`dataSet`	An `AffymetrixCelSet`.
`...`	Arguments passed to the constructor of `ProbeLevelTransform`.
`model`	A `character` string for quickly specifying default parameter settings.
`rescaleBy`	A `character` string specifying what sets of cells should be rescaled towards a target average, if any. Default is to rescale all cells together. If `"none"`, no rescaling is done.
`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 `rescaleBy != "none"`.
`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 `NULL`, all probes are considered.
`mergeShifts`	If `TRUE`, the shift of the probe sequence relative to the SNP position is ignored, otherwise not.
`B`	An `integer` specifying by how many nucleotides the allelic groups should be stratified by. If zero, all SNPs are put in one group.
`flavor`	A `character` string specifying what algorithm is used to fit the crosstalk calibration.
`alpha`, `q`, `Q`, `lambda`	Model fitting parameters.
`pairBy`	A `character` string specifying how allele probe pairs are identified.

What probe signals are updated?

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.

What probe signals are used to fit model?

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.

Important about rescaling towards 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").

Fields and Methods

Methods:

	`process`	-

Methods inherited from ProbeLevelTransform:
getRootPath

Methods inherited from Transform:
getOutputDataSet, getOutputFiles

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Author(s)

Henrik Bengtsson

The AromaChipTypeAnnotationFile class

Description

Package: aroma.affymetrix
Class 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.

Usage

AromaChipTypeAnnotationFile(...)
AromaChipTypeAnnotationFile(...)

Arguments

...

Arguments passed to AffymetrixFile.

Fields and Methods

Methods:

	`byChipType`	-
	`getChipType`	-
	`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

Author(s)

Henrik Bengtsson

The ArrayExplorer class

Description

Package: aroma.affymetrix
Class ArrayExplorer

Object
~~|
~~+--Explorer
~~~~~~~|
~~~~~~~+--ArrayExplorer

Directly known subclasses:

public abstract static class ArrayExplorer
extends Explorer

Usage

ArrayExplorer(csTuple=NULL, ...)
ArrayExplorer(csTuple=NULL, ...)

Arguments

`csTuple`	An `AffymetrixCelSet` object.
`...`	Not used.

Fields and Methods

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

Author(s)

Henrik Bengtsson

The AvgCnPlm class

Description

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

Usage

AvgCnPlm(..., combineAlleles=FALSE)
AvgCnPlm(..., combineAlleles=FALSE)

Arguments

`...`	Arguments passed to `AvgSnpPlm`.
`combineAlleles`	If `FALSE`, allele A and allele B are treated separately, otherwise together.

Fields and Methods

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 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

Author(s)

Henrik Bengtsson

The AvgPlm class

Description

Package: aroma.affymetrix
Class 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.

Usage

AvgPlm(..., flavor=c("median", "mean"))
AvgPlm(..., flavor=c("median", "mean"))

Arguments

`...`	Arguments passed to `ProbeLevelModel`.
`flavor`	A `character` string specifying what model fitting algorithm to be used. This makes it possible to get identical estimates as other packages.

Fields and Methods

Methods:
No methods defined.

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

Model

For a single unit group, the averaging PLM of K probes is:

$y_{ik} = \theta_i + \varepsilon_{ik}$

where $\theta_i$ are the chip effects for arrays $i=1,...,I$ . The $\varepsilon_{ik}$ are zero-mean noise with equal variance.

Different flavors of model fitting

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.

$\hat{\theta}_{i} = 1/K \sum_k y_{ik}$

Use argument flavor="median" to fit the model robustly, i.e.

$\hat{\theta}_{i} = median_k y_{ik}$

Missing values are always excluded.

Author(s)

Henrik Bengtsson

The AvgSnpPlm class

Description

Package: aroma.affymetrix
Class AvgSnpPlm

Directly known subclasses:
AvgCnPlm

public abstract static class AvgSnpPlm
extends SnpPlm

Usage

AvgSnpPlm(..., mergeStrands=FALSE)
AvgSnpPlm(..., mergeStrands=FALSE)

Arguments

`...`	Arguments passed to `AvgPlm`.
`mergeStrands`	If `TRUE`, the sense and the anti-sense strands are fitted together, otherwise separately.

Fields and Methods

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 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

Author(s)

Henrik Bengtsson

The BackgroundCorrection class

Description

Package: aroma.affymetrix
Class BackgroundCorrection

Directly known subclasses:
GcRmaBackgroundCorrection, LimmaBackgroundCorrection, NormExpBackgroundCorrection, OpticalBackgroundCorrection, RmaBackgroundCorrection

public abstract static class BackgroundCorrection
extends ProbeLevelTransform

This class represents a background adjustment function.

Usage

BackgroundCorrection(..., subsetToUpdate=NULL, typesToUpdate=NULL)
BackgroundCorrection(..., subsetToUpdate=NULL, typesToUpdate=NULL)

Arguments

`...`	Arguments passed to the constructor of `ProbeLevelTransform`.
`subsetToUpdate`	The probes to be updated. If `NULL`, all probes are updated.
`typesToUpdate`	Types of probes to be updated.

Fields and Methods

Methods:

	`process`	-

Methods inherited from ProbeLevelTransform:
getRootPath

Methods inherited from Transform:
getOutputDataSet, getOutputFiles

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Author(s)

Ken Simpson, Henrik Bengtsson

The BaseCountNormalization class

Description

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.

Usage

BaseCountNormalization(..., model=c("robustSmoothSpline", "lm"), bootstrap=FALSE)
BaseCountNormalization(..., model=c("robustSmoothSpline", "lm"), bootstrap=FALSE)

Arguments

`...`	Arguments passed to the constructor of `AbstractProbeSequenceNormalization`.
`model`	A `character` string specifying the model used to fit the base-count effects.
`bootstrap`	If `TRUE`, the model fitting is done by bootstrap in order to save memory.

Fields and Methods

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 ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Requirements

This class requires that an aroma probe sequence file is available for the chip type.

Author(s)

Henrik Bengtsson

The BasePositionNormalization class

Description

Package: aroma.affymetrix
Class 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.

Usage

BasePositionNormalization(..., model=c("smooth.spline"), df=5)
BasePositionNormalization(..., model=c("smooth.spline"), df=5)

Arguments

`...`	Arguments passed to the constructor of `LinearModelProbeSequenceNormalization`.
`model`	A `character` string specifying the model used to fit the base-count effects.
`df`	The degrees of freedom of the model.

Fields and Methods

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 ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Author(s)

Henrik Bengtsson, Mark Robinson

The ChipEffectFile class

Description

Package: aroma.affymetrix
Class 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.

Usage

ChipEffectFile(..., probeModel=c("pm"))
ChipEffectFile(..., probeModel=c("pm"))

Arguments

`...`	Arguments passed to `ParameterCelFile`.
`probeModel`	The specific type of model, e.g. `"pm"`.

Fields and Methods

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 AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Author(s)

Henrik Bengtsson

The ChipEffectSet class

Description

Package: aroma.affymetrix
Class 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.

Usage

ChipEffectSet(..., probeModel=c("pm"))
ChipEffectSet(..., probeModel=c("pm"))

Arguments

`...`	Arguments passed to `AffymetrixCelSet`.
`probeModel`	The specific type of model, e.g. `"pm"`.

Fields and Methods

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

Author(s)

Henrik Bengtsson

The ChipEffectTransform class

Description

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.

Usage

ChipEffectTransform(dataSet=NULL, ...)
ChipEffectTransform(dataSet=NULL, ...)

Arguments

`dataSet`	The input data set as an `ChipEffectSet`.
`...`	Arguments passed to the constructor of `Transform`.

Details

Subclasses must implement the process() method.

Fields and Methods

Methods:
No methods defined.

Methods inherited from Transform:
getOutputDataSet, getOutputFiles

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Author(s)

Henrik Bengtsson

The CnagCfhFile class

Description

Package: aroma.affymetrix
Class CnagCfhFile

Directly known subclasses:

public abstract static class CnagCfhFile
extends AffymetrixFile

A CnagCfhFile object represents a single CNAG CFH file.

Usage

CnagCfhFile(..., cdf=NULL)
CnagCfhFile(..., cdf=NULL)

Arguments

`...`	Arguments passed to `AromaMicroarrayDataFile`.
`cdf`	An optional `AffymetrixCdfFile`

Fields and Methods

Methods:

	`getCdf`	-
	`nbrOfCells`	-
	`nbrOfSnps`	-
	`setCdf`	-

Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Author(s)

Henrik Bengtsson

The CnagCfhSet class

Description

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.

Usage

CnagCfhSet(files=NULL, ...)
CnagCfhSet(files=NULL, ...)

Arguments

`files`	A `list` of `CnagCfhFile`:s.
`...`	Not used.

Fields and Methods

Methods:

	`as`	-
	`as.CnagCfhSet`	-
	`byName`	-
	`getAverage`	-
	`getAverageAsinh`	-
	`getAverageFile`	-
	`getAverageLog`	-
	`getCdf`	-
	`getData`	-
	`getTimestamps`	-
	`readUnits`	-
	`setCdf`	-

Author(s)

Henrik Bengtsson

The CnChipEffectFile class

Description

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.

Usage

CnChipEffectFile(..., combineAlleles=FALSE)
CnChipEffectFile(..., combineAlleles=FALSE)

Arguments

`...`	Arguments passed to `SnpChipEffectFile`.
`combineAlleles`	A `logical` indicating if the signals from allele A and allele B are combined or not.

Fields and Methods

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 AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Author(s)

Henrik Bengtsson

The CnChipEffectSet class

Description

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.

Usage

CnChipEffectSet(..., combineAlleles="byFirstFile")
CnChipEffectSet(..., combineAlleles="byFirstFile")

Arguments

`...`	Arguments passed to `SnpChipEffectSet`.
`combineAlleles`	A `logical` indicating if the signals from allele A and allele B are combined or not.

Fields and Methods

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 AffymetrixFileSet:
as, as.AffymetrixFileSet, byPath, getDefaultFullName

Author(s)

Henrik Bengtsson

The CnPlm class

Description

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.

Usage

CnPlm(...)
CnPlm(...)

Arguments

...

Arguments passed to SnpPlm.

Details

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

Methods:

	`getCellIndices`	-
	`getChipEffectSet`	-
	`getCombineAlleles`	-
	`getProbeAffinityFile`	-
	`setCombineAlleles`	-

Methods inherited from SnpPlm:
getCellIndices, getChipEffectSet, getMergeStrands, getParameters, getProbeAffinityFile, setMergeStrands

Methods inherited from Interface:
extend, print, uses

Requirements

Classes inheriting from this Interface must provide the following fields, in addition to the ones according to SnpPlm:

combineAlleles: A logical indicating if total or allele-specific copy numbers should be estimated according to the above averaging.

Author(s)

Henrik Bengtsson

The CnProbeAffinityFile class

Description

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.

Usage

CnProbeAffinityFile(..., combineAlleles=FALSE)
CnProbeAffinityFile(..., combineAlleles=FALSE)

Arguments

`...`	Arguments passed to `SnpProbeAffinityFile`.
`combineAlleles`	If `FALSE`, allele A and allele B are treated separately, otherwise together.

Fields and Methods

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 AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Author(s)

Henrik Bengtsson

The CrlmmParametersFile class

Description

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.

Usage

CrlmmParametersFile(...)
CrlmmParametersFile(...)

Arguments

...

Arguments passed to AromaUnitSignalBinaryFile.

Fields and Methods

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 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

Author(s)

Henrik Bengtsson

The CrlmmParametersSet class

Description

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 CrlmmParametersFiles with identical chip types.

Usage

CrlmmParametersSet(...)
CrlmmParametersSet(...)

Arguments

...

Arguments passed to AromaUnitSignalBinarySet.

Fields and Methods

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

Author(s)

Henrik Bengtsson

The DChipCdfBinFile class

Description

Package: aroma.affymetrix
Class DChipCdfBinFile

Directly known subclasses:

public abstract static class DChipCdfBinFile
extends UnitNamesFile

A DChipCdfBinFile object represents a DChip CDF.bin file.

Usage

DChipCdfBinFile(...)
DChipCdfBinFile(...)

Arguments

...

Arguments passed to AffymetrixFile.

Fields and Methods

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 AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Author(s)

Henrik Bengtsson

The DChipDcpFile class

Description

Package: aroma.affymetrix
Class DChipDcpFile

Directly known subclasses:

public abstract static class DChipDcpFile
extends AffymetrixFile

A DChipDcpFile object represents a DChip DCP file.

Usage

DChipDcpFile(...)
DChipDcpFile(...)

Arguments

...

Arguments passed to AffymetrixFile.

Fields and Methods

Methods:

	`dim`	-
	`extractTheta`	-
	`getCalls`	-
	`getExcludes`	-
	`getFileFormat`	-
	`getHeader`	-
	`getNormalizedIntensities`	-
	`getRawIntensities`	-
	`getThetaStds`	-
	`getThetas`	-
	`getThetasAB`	-
	`hasMbeiData`	-
	`hasNormalizedData`	-
	`nbrOfCells`	-
	`nbrOfUnits`	-

Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Author(s)

Henrik Bengtsson

The DChipDcpSet class

Description

Package: aroma.affymetrix
Class 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.

Usage

DChipDcpSet(files=NULL, ...)
DChipDcpSet(files=NULL, ...)

Arguments

`files`	A `list` of `DChipDcpFile`:s.
`...`	Not used.

Fields and Methods

Methods:

	`as`	-
	`as.DChipDcpSet`	-
	`byName`	-
	`exportTotalAndFracB`	-
	`extractTheta`	-
	`getCdfBin`	-
	`getChipType`	-

Methods inherited from AffymetrixFileSet:
as, as.AffymetrixFileSet, byPath, getDefaultFullName

Author(s)

Henrik Bengtsson

The DChipGenomeInformation class

Description

Package: aroma.affymetrix
Class 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.

Usage

DChipGenomeInformation(...)
DChipGenomeInformation(...)

Arguments

...

Arguments passed to GenomeInformation.

Details

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.

Fields and Methods

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

Author(s)

Henrik Bengtsson

The DChipQuantileNormalization class

Description

Package: aroma.affymetrix
Class DChipQuantileNormalization

Directly known subclasses:

public static class DChipQuantileNormalization
extends QuantileNormalization

This class represents a special QuantileNormalization using smooth-splines.

Usage

DChipQuantileNormalization(..., robust=FALSE)
DChipQuantileNormalization(..., robust=FALSE)

Arguments

`...`	Arguments passed to the constructor of `QuantileNormalization`.
`robust`	If `TRUE`, the normalization function is estimated robustly, otherwise not.

Details

This normalization method implements the two-pass algorithm described in Bengtsson et al. (2008).

Fields and Methods

Methods:

	`process`	-

Methods inherited from QuantileNormalization:
findTargetDistributionFile, getParameters, process

Methods inherited from ProbeLevelTransform:
getRootPath

Methods inherited from Transform:
getOutputDataSet, getOutputFiles

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Author(s)

Henrik Bengtsson

References

[1] H. Bengtsson, R. Irizarry, B. Carvalho, & T.P. Speed. Estimation and assessment of raw copy numbers at the single locus level, Bioinformatics, 2008.

The DChipSnpInformation class

Description

Package: aroma.affymetrix
Class 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.

Usage

DChipSnpInformation(...)
DChipSnpInformation(...)

Arguments

...

Arguments passed to SnpInformation.

Details

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.

Fields and Methods

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

Author(s)

Henrik Bengtsson

Estimation and assessment of raw copy numbers at the single locus level (CRMA v1)

Description

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.

Usage

  ## 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(...)

Arguments

`csR`, `dataSet`	An `AffymetrixCelSet` (or the name of an `AffymetrixCelSet`).
`shift`	An tuning parameter specifying how much to shift the probe signals before probe summarization.
`combineAlleles`	A `logical` specifying whether allele probe pairs should be summed before modeling or not.
`lengthRange`	An optional `numeric` vector of length two passed to `FragmentLengthNormalization`.
`arrays`	A `integer` `vector` specifying the subset of arrays to process. If `NULL`, all arrays are considered.
`drop`	If `TRUE`, the summaries are returned, otherwise a named `list` of all intermediate and final results.
`verbose`	See `Verbose`.
`...`	Additional arguments used to set up `AffymetrixCelSet` (when argument `dataSet` is specified).

Value

Returns a named list, iff drop == FALSE, otherwise only ChipEffectSet object.

Allele-specific or only total-SNP signals

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).

Author(s)

Henrik Bengtsson

References

[1] H. Bengtsson, R. Irizarry, B. Carvalho & T.P. Speed. Estimation and assessment of raw copy numbers at the single locus level, Bioinformatics, 2008.

A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays (CRMA v2)

Description

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.

Usage

  ## 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(...)

Arguments

`csR`, `dataSet`	An `AffymetrixCelSet` (or the name of an `AffymetrixCelSet`).
`combineAlleles`	A `logical` specifying whether allele probe pairs should be summed before modeling or not.
`lengthRange`	An optional `numeric` vector of length two passed to `FragmentLengthNormalization`.
`arrays`	A `integer` `vector` specifying the subset of arrays to process. If `NULL`, all arrays are considered.
`plm`	A `character` string specifying which type of probe-summarization model to used.
`drop`	If `TRUE`, the summaries are returned, otherwise a named `list` of all intermediate and final results.
`verbose`	See `Verbose`.
`...`	Additional arguments used to set up `AffymetrixCelSet` (when argument `dataSet` is specified).

Value

Returns a named list, iff drop == FALSE, otherwise only ChipEffectSet object.

Allele-specific or only total-SNP signals

doASCRMAv2(...) is a wrapper for doCRMAv2(..., combineAlleles=FALSE).

Author(s)

Henrik Bengtsson

References

[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.

Finding Isoforms using Robust Multichip Analysis (FIRMA)

Description

Finding Isoforms using Robust Multichip Analysis (FIRMA) based on [1].

Usage

  ## 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)

Arguments

`csR`, `dataSet`	An `AffymetrixCelSet` (or the name of an `AffymetrixCelSet`).
`...`	Additional arguments passed to `FirmaModel`, and to set up `AffymetrixCelSet` (when argument `dataSet` is specified).
`flavor`	A `character` string specifying the flavor of FIRMA to use.
`drop`	If `TRUE`, the FIRMA scores are returned, otherwise a named `list` of all intermediate and final results.
`verbose`	See `Verbose`.

Value

Returns a named list, iff drop == FALSE, otherwise only FirmaSet object (containing the FIRMA scores).

Using a custom exon-by-transcript CDF

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').

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.

Author(s)

Henrik Bengtsson

References

[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)

Description

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.

Usage

  ## 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)

Arguments

`csR`, `dataSet`	An `AffymetrixCelSet` (or the name of an `AffymetrixCelSet`).
`arrays`	A `integer` `vector` specifying the subset of arrays to process. If `NULL`, all arrays are considered.
`type`	A `character` string specifying what type of model to use for the GCRMA background correction. For more details, see `GcRmaBackgroundCorrection`.
`uniquePlm`	If `TRUE`, the log-additive probe-summarization model is done on probeset with unique sets of probes. If `FALSE`, the summarization is done on "as-is" probesets as specified by the CDF.
`drop`	If `TRUE`, the summaries are returned, otherwise a named `list` of all intermediate and final results.
`verbose`	See `Verbose`.
`...`	Additional arguments used to set up `AffymetrixCelSet` (when argument `dataSet` is specified).

Value

Returns a named list, iff drop == FALSE, otherwise only ChipEffectSet object.

Author(s)

Henrik Bengtsson

References

[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)

Description

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.

Usage

  ## 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)

Arguments

`csR`, `dataSet`	An `AffymetrixCelSet` (or the name of an `AffymetrixCelSet`).
`arrays`	A `integer` `vector` specifying the subset of arrays to process. If `NULL`, all arrays are considered.
`flavor`	A character string specifying what model fitting algorithm to be used, cf. `RmaPlm`.
`uniquePlm`	If `TRUE`, the log-additive probe-summarization model is done on probeset with unique sets of probes. If `FALSE`, the summarization is done on "as-is" probesets as specified by the CDF.
`drop`	If `TRUE`, the summaries are returned, otherwise a named `list` of all intermediate and final results.
`verbose`	See `Verbose`.
`...`	Additional arguments used to set up `AffymetrixCelSet` (when argument `dataSet` is specified).

Value

Returns a named list, iff drop == FALSE, otherwise only ChipEffectSet object.

Author(s)

Henrik Bengtsson

References

[1] Irizarry et al. Summaries of Affymetrix GeneChip probe level data. NAR, 2003, 31, e15.

The ExonChipEffectFile class

Description

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.

Usage

ExonChipEffectFile(..., mergeGroups=FALSE)
ExonChipEffectFile(..., mergeGroups=FALSE)

Arguments

`...`	Arguments passed to `ChipEffectFile`.
`mergeGroups`	Specifies if the groups are merged or not for these estimates.

Fields and Methods

Methods:

	`readUnits`	-

Methods inherited from ParameterCelFile:
extractDataFrame, extractMatrix, readUnits

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Author(s)

Ken Simpson, Henrik Bengtsson

The ExonChipEffectSet class

Description

Package: aroma.affymetrix
Class ExonChipEffectSet

Directly known subclasses:

public static class ExonChipEffectSet
extends ChipEffectSet

This class represents estimates of chip effects in the probe-level models.

Usage

ExonChipEffectSet(..., mergeGroups=TRUE)
ExonChipEffectSet(..., mergeGroups=TRUE)

Arguments

`...`	Arguments passed to `ChipEffectSet`.
`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.

Fields and Methods

Methods:

	`findUnitsTodo`	-
	`getAverageFile`	-
	`getMergeGroups`	-
	`setMergeGroups`	-

Methods inherited from ParameterCelSet:
extractDataFrame, extractMatrix

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Methods inherited from AffymetrixFileSet:
as, as.AffymetrixFileSet, byPath, getDefaultFullName

Author(s)

Ken Simpson, Henrik Bengtsson

The ExonProbeAffinityFile class

Description

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.

Usage

ExonProbeAffinityFile(..., mergeGroups=FALSE)
ExonProbeAffinityFile(..., mergeGroups=FALSE)

Arguments

`...`	Arguments passed to `ProbeAffinityFile`.
`mergeGroups`	Specifies if the groups (exons) are merged or not for these estimates.

Fields and Methods

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 AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Author(s)

Ken Simpson, Henrik Bengtsson

The ExonRmaPlm class

Description

Package: aroma.affymetrix
Class 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).

Usage

ExonRmaPlm(..., mergeGroups=TRUE)
ExonRmaPlm(..., mergeGroups=TRUE)

Arguments

`...`	Arguments passed to `RmaPlm`.
`mergeGroups`	A `logical` flag specifying whether to merge exons into transcripts.

Fields and Methods

Methods:

	`getCellIndices`	-
	`getChipEffectSet`	-
	`getProbeAffinityFile`	-
	`setMergeGroups`	-

Methods inherited from RmaPlm:
getAsteriskTags, getCalculateResidualsFunction, getParameters, getRlmFitFunctions

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

Model

RmaPlm.

Author(s)

Ken Simpson, Henrik Bengtsson, Elizabeth Purdom

References

Irizarry et al. Summaries of Affymetrix GeneChip probe level data. NAR, 2003, 31, e15.

The FirmaFile class

Description

Package: aroma.affymetrix
Class FirmaFile

Directly known subclasses:

public abstract static class FirmaFile
extends ParameterCelFile

This class represents scores calculated by the FIRMA algorithm.

Usage

FirmaFile(...)
FirmaFile(...)

Arguments

...

Arguments passed to AffymetrixCelFile.

Fields and Methods

Methods:

	`extractMatrix`	-
	`findUnitsTodo`	-
	`readUnits`	-

Methods inherited from ParameterCelFile:
extractDataFrame, extractMatrix, readUnits

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Author(s)

Ken Simpson, Henrik Bengtsson

The FirmaModel class

Description

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.

Usage

FirmaModel(rmaPlm=NULL, summaryMethod=c("median", "upperQuartile", "max"),
  operateOn=c("residuals", "weights"), ...)
FirmaModel(rmaPlm=NULL, summaryMethod=c("median", "upperQuartile", "max"),
  operateOn=c("residuals", "weights"), ...)

Arguments

`rmaPlm`	An @RmaPlm object.
`summaryMethod`	A `character` specifying what summarization method should be used.
`operateOn`	A `character` specifying what statistic to operate on.
`...`	Arguments passed to constructor of `UnitModel`.

Fields and Methods

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

Author(s)

Ken Simpson, Henrik Bengtsson

The FirmaSet class

Description

Package: aroma.affymetrix
Class FirmaSet

Directly known subclasses:

public static class FirmaSet
extends ParameterCelSet

Usage

FirmaSet(...)
FirmaSet(...)

Arguments

...

Arguments passed to constructor of AffymetrixCelSet.

Fields and Methods

Methods:

	`extractMatrix`	-
	`findUnitsTodo`	-
	`getCellIndices`	-
	`readUnits`	-

Methods inherited from ParameterCelSet:
extractDataFrame, extractMatrix

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Methods inherited from AffymetrixFileSet:
as, as.AffymetrixFileSet, byPath, getDefaultFullName

Author(s)

Ken Simpson, Henrik Bengtsson

The FragmentEquivalentClassNormalization class

Description

Package: aroma.affymetrix
Class 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.

Usage

FragmentEquivalentClassNormalization(dataSet=NULL, ..., targetAvgs=NULL,
  subsetToFit="-XY")
FragmentEquivalentClassNormalization(dataSet=NULL, ..., targetAvgs=NULL,
  subsetToFit="-XY")

Arguments

`dataSet`	A `CnChipEffectSet`.
`...`	Additional arguments passed to the constructor of `ChipEffectTransform`.
`targetAvgs`	An optional list of `function`s. For each enzyme there is one target averages to which all arrays should be normalized to.
`subsetToFit`	The units from which the normalization curve should be estimated. If `NULL`, all are considered.

Fields and Methods

Methods:

	`getAromaUfcFile`	-
	`getCdf`	-
	`process`	-

Methods inherited from ChipEffectTransform:
getRootPath

Methods inherited from Transform:
getOutputDataSet, getOutputFiles

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Requirements

This class requires an UFC (Unit Fragment Class) annotation file.

Acknowledgments

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.

Author(s)

Henrik Bengtsson

The FragmentLengthNormalization class

Description

Package: aroma.affymetrix
Class 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.

Usage

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)

Arguments

`dataSet`	A `SnpChipEffectSet`.
`...`	Additional arguments passed to the constructor of `ChipEffectTransform`.
`target`	(Optional) A `character` string or a list of `function`s specifying what to normalize toward. For each enzyme there is one target function to which all arrays should be normalized to.
`subsetToFit`	The units from which the normalization curve should be estimated. If `NULL`, all are considered.
`lengthRange`	If given, a `numeric` `vector` of length 2 specifying the range of fragment lengths considered. All fragments with lengths outside this range are treated as if they were missing.
`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.

Details

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.

Fields and Methods

Methods:

	`getCdf`	-
	`process`	-

Methods inherited from ChipEffectTransform:
getRootPath

Methods inherited from Transform:
getOutputDataSet, getOutputFiles

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Requirements

This class requires a SNP information annotation file for the chip type to be normalized.

Author(s)

Henrik Bengtsson

The GcContentNormalization class

Description

Package: aroma.affymetrix
Class GcContentNormalization

Directly known subclasses:

public static class GcContentNormalization
extends ChipEffectTransform

Usage

GcContentNormalization(dataSet=NULL, ..., targetFunction=NULL, subsetToFit=NULL)
GcContentNormalization(dataSet=NULL, ..., targetFunction=NULL, subsetToFit=NULL)

Arguments

`dataSet`	A `CnChipEffectSet`.
`...`	Additional arguments passed to the constructor of `ChipEffectTransform`.
`targetFunction`	A `function`. The target function to which all arrays should be normalized to.
`subsetToFit`	The units from which the normalization curve should be estimated. If `NULL`, all are considered.

Fields and Methods

Methods:

	`getCdf`	-
	`process`	-

Methods inherited from ChipEffectTransform:
getRootPath

Methods inherited from Transform:
getOutputDataSet, getOutputFiles

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Requirements

This class requires an Aroma unit GC-content (UGC) file.

Author(s)

Henrik Bengtsson

The GcContentNormalization2 class

Description

Package: aroma.affymetrix
Class 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.

Usage

GcContentNormalization2(...)
GcContentNormalization2(...)

Arguments

...

Arguments passed to the constructor of AdditiveCovariatesNormalization.

Fields and Methods

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 ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Author(s)

Henrik Bengtsson

The GcRmaBackgroundCorrection class

Description

Package: aroma.affymetrix
Class GcRmaBackgroundCorrection

Directly known subclasses:

public static class GcRmaBackgroundCorrection
extends BackgroundCorrection

This class represents the GCRMA background adjustment function.

Usage

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

`...`	Arguments passed to the constructor of `ProbeLevelTransform`.
`indicesNegativeControl`	Locations of any negative control probes (e.g., the anti-genomic controls on the human exon array). If `NULL` and `type == "affinities"`, then all non-PM probes are used as the negative controls.
`affinities`	A `numeric` `vector` of probe affinities, usually as calculated by `computeAffinities()` of the `AffymetrixCdfFile` class.
`type`	Type (flavor) of background correction, which can be either `"fullmodel"` (uses MMs; requires that the chip type has PM/MM pairs) or `"affinities"` (uses probe sequence only).
`gsbAdjust`	If `TRUE`, adjustment for specific binding is done, otherwise not.
`opticalAdjust`	If `TRUE`, correction for optical effect is done first, utilizing `OpticalBackgroundCorrection`.
`gsbParameters`	Additional argument passed to the internal `bgAdjustGcrma()` method.
`seed`	An (optional) `integer` specifying a temporary random seed to be used during processing. The random seed is set to its original state when done. If `NULL`, it is not set.

Fields and Methods

Methods:

	`process`	-

Methods inherited from BackgroundCorrection:
getParameters, process

Methods inherited from ProbeLevelTransform:
getRootPath

Methods inherited from Transform:
getOutputDataSet, getOutputFiles

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Author(s)

Ken Simpson, Henrik Bengtsson

References

[1] Z. Wu, R. Irizarry, R. Gentleman, F.M. Murillo & F. Spencer. A Model Based Background Adjustment for Oligonucleotide Expression Arrays, JASA, 2004.

The GenericReporter class

Description

Package: aroma.affymetrix
Class GenericReporter

Object
~~|
~~+--GenericReporter

Directly known subclasses:
AffymetrixCelSetReporter, AffymetrixFileSetReporter, SpatialReporter

public abstract static class GenericReporter
extends Object

Usage

GenericReporter(tags="*", ...)
GenericReporter(tags="*", ...)

Arguments

`tags`	A `character` `vector` of tags to be added to the output path.
`...`	Not used.

Fields and Methods

Methods:

	`getFullName`	-
	`getName`	-
	`getPath`	-
	`getTags`	-
	`process`	-
	`setup`	-

Author(s)

Henrik Bengtsson

The GenomeInformation class

Description

Package: aroma.affymetrix
Class GenomeInformation

Directly known subclasses:
AffymetrixCsvGenomeInformation, DChipGenomeInformation, UgpGenomeInformation

public abstract static class GenomeInformation
extends FileCacheKeyInterface

Usage

GenomeInformation(..., .verify=TRUE)
GenomeInformation(..., .verify=TRUE)

Arguments

`...`	Arguments passed to `GenericDataFile`.
`.verify`	For internal use only.

Fields and Methods

Methods:

	`byChipType`	-
	`getChipType`	-
	`getChromosomeStats`	-
	`getChromosomes`	-
	`getData`	-
	`getPositions`	-
	`getUnitsOnChromosome`	-
	`getUnitsOnChromosomes`	-
	`nbrOfUnits`	-
	`plotDensity`	-

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Author(s)

Henrik Bengtsson

The HetLogAddCnPlm class

Description

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

Usage

HetLogAddCnPlm(..., combineAlleles=FALSE)
HetLogAddCnPlm(..., combineAlleles=FALSE)

Arguments

`...`	Arguments passed to `HetLogAddCnPlm`.
`combineAlleles`	If `FALSE`, allele A and allele B are treated separately, otherwise together.

Fields and Methods

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 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

Model

TO DO.

Author(s)

Henrik Bengtsson

The HetLogAddPlm class

Description

Package: aroma.affymetrix
Class 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.

Usage

HetLogAddPlm(...)
HetLogAddPlm(...)

Arguments

...

Arguments passed to RmaPlm.

Fields and Methods

Methods:
No methods defined.

Methods inherited from RmaPlm:
getAsteriskTags, getCalculateResidualsFunction, getParameters, getRlmFitFunctions

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

Author(s)

Henrik Bengtsson

The HetLogAddSnpPlm class

Description

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

Usage

HetLogAddSnpPlm(..., mergeStrands=FALSE)
HetLogAddSnpPlm(..., mergeStrands=FALSE)

Arguments

`...`	Arguments passed to `HetLogAddPlm`.
`mergeStrands`	If `TRUE`, the sense and the anti-sense strands are fitted together, otherwise separately.

Fields and Methods

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 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

Author(s)

Henrik Bengtsson

Robust Multichip Analysis (RMA) reproducing the affy package

Description

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).

Usage

  ## 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(...)

Arguments

`csR`	An `AffymetrixCelSet`.
`flavor`	A `character` string specifying the estimators used in the RMA summarization step.
`...`	Additional arguments passed to `doRMA`() used internally.
`verbose`	See `Verbose`.

Value

Returns an annotated ExpressionSet.

Reproducibility of affy

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.

Author(s)

Henrik Bengtsson

References

[1] Irizarry et al. Summaries of Affymetrix GeneChip probe level data. NAR, 2003, 31, e15.

The LimmaBackgroundCorrection class

Description

Package: aroma.affymetrix
Class LimmaBackgroundCorrection

Directly known subclasses:
NormExpBackgroundCorrection

public static class LimmaBackgroundCorrection
extends BackgroundCorrection

This class represents the various "background" correction methods implemented in the limma package.

Usage

LimmaBackgroundCorrection(..., args=NULL, addJitter=FALSE, jitterSd=0.2, seed=6022007)
LimmaBackgroundCorrection(..., args=NULL, addJitter=FALSE, jitterSd=0.2, seed=6022007)

Arguments

`...`	Arguments passed to the constructor of `BackgroundCorrection`.
`args`	A `list` of additional arguments passed to the correction algorithm.
`addJitter`	If `TRUE`, Zero-mean gaussian noise is added to the signals before being background corrected.
`jitterSd`	Standard deviation of the jitter noise added.
`seed`	An (optional) `integer` specifying a temporary random seed to be used for generating the (optional) jitter. The random seed is set to its original state when done. If `NULL`, it is not set.

Details

By default, only PM signals are background corrected and MMs are left unchanged.

Fields and Methods

Methods:

	`process`	-

Methods inherited from BackgroundCorrection:
getParameters, process

Methods inherited from ProbeLevelTransform:
getRootPath

Methods inherited from Transform:
getOutputDataSet, getOutputFiles

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Jitter noise

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.

Author(s)

Henrik Bengtsson. Adopted from RmaBackgroundCorrection by Ken Simpson.

The LinearModelProbeSequenceNormalization class

Description

Package: aroma.affymetrix
Class 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.

Usage

LinearModelProbeSequenceNormalization(...)
LinearModelProbeSequenceNormalization(...)

Arguments

...

Arguments passed to the constructor of AbstractProbeSequenceNormalization.

Fields and Methods

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 ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Requirements

This class requires that an aroma probe sequence file is available for the chip type.

Memory usage

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.

Author(s)

Henrik Bengtsson

The MatNormalization class

Description

Package: aroma.affymetrix
Class 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].

Usage

MatNormalization(..., unitsToFit=NULL, model=c("lm"), nbrOfBins=200)
MatNormalization(..., unitsToFit=NULL, model=c("lm"), nbrOfBins=200)

Arguments

`...`	Arguments passed to the constructor of `AbstractProbeSequenceNormalization`.
`unitsToFit`	The units from which the normalization curve should be estimated. If `NULL`, all are considered.
`model`	A `character` string specifying the model used to fit the base-count effects.
`nbrOfBins`	The number of bins to use for the variance smoothing step.

Fields and Methods

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 ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Requirements

This class requires that an aroma probe sequence file and aroma match scores file is available for the chip type.

Author(s)

Mark Robinson

References

[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.

The MatSmoothing class

Description

Package: aroma.affymetrix
Class MatSmoothing

Directly known subclasses:

public static class MatSmoothing
extends ProbeLevelTransform

This class represents a function for smoothing data with a trimmed mean.

Usage

MatSmoothing(..., design=NULL, probeWindow=300, nProbes=10, meanTrim=0.1)
MatSmoothing(..., design=NULL, probeWindow=300, nProbes=10, meanTrim=0.1)

Arguments

`...`	Arguments passed to `ProbeLevelTransform`.
`design`	A design `matrix`.
`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].

Fields and Methods

Methods:

	`process`	-

Methods inherited from ProbeLevelTransform:
getRootPath

Methods inherited from Transform:
getOutputDataSet, getOutputFiles

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Author(s)

Mark Robinson, Henrik Bengtsson

The MbeiCnPlm class

Description

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

Usage

MbeiCnPlm(..., combineAlleles=FALSE)
MbeiCnPlm(..., combineAlleles=FALSE)

Arguments

`...`	Arguments passed to `MbeiSnpPlm`.
`combineAlleles`	If `FALSE`, allele A and allele B are treated separately, otherwise together.

Fields and Methods

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 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

Author(s)

Henrik Bengtsson

The MbeiPlm class

Description

Package: aroma.affymetrix
Class 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).

Usage

MbeiPlm(...)
MbeiPlm(...)

Arguments

...

Arguments passed to ProbeLevelModel.

Fields and Methods

Methods:
No methods defined.

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

Model

For a single unit group, the multiplicative model is:

$y_{ik} = \theta_i \phi_k + \varepsilon_{ik}$

where $\theta_i$ are the chip effects for arrays $i=1,...,I$ , and $\phi_k$ are the probe affinities for probes $k=1,...,K$ . The $\varepsilon_{ik}$ are zero-mean noise with equal variance. To make to parameters identifiable, the constraint $\prod_k \phi_k = 1$ is added.

Author(s)

Henrik Bengtsson

References

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.

The MbeiSnpPlm class

Description

Package: aroma.affymetrix
Class MbeiSnpPlm

Directly known subclasses:
MbeiCnPlm

public abstract static class MbeiSnpPlm
extends SnpPlm

Usage

MbeiSnpPlm(..., mergeStrands=FALSE)
MbeiSnpPlm(..., mergeStrands=FALSE)

Arguments

`...`	Arguments passed to `MbeiPlm`.
`mergeStrands`	If `TRUE`, the sense and the anti-sense strands are fitted together, otherwise separately.

Fields and Methods

Methods:
No methods defined.

Methods inherited from SnpPlm:
getCellIndices, getChipEffectSet, getMergeStrands, getParameters, getProbeAffinityFile, setMergeStrands

Methods inherited from MbeiPlm:
getAsteriskTags, getFitUnitGroupFunction

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

Author(s)

Henrik Bengtsson

The Model class

Description

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.

Usage

Model(dataSet=NULL, tags="*", ..., .onUnknownArgs=c("error", "warning", "ignore"))
Model(dataSet=NULL, tags="*", ..., .onUnknownArgs=c("error", "warning", "ignore"))

Arguments

`dataSet`	The data set to which this model should be fitted.
`tags`	A `character` `vector` of tags to be appended to the tags of the input data set.
`...`	Not used.
`.onUnknownArgs`	A `character` string specifying what should occur if there are unknown arguments in `...`.

Fields and Methods

Methods:

	`fit`	-
	`getAsteriskTags`	-
	`getDataSet`	-
	`getFullName`	-
	`getName`	-
	`getPath`	-
	`getTags`	-
	`setTags`	-

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Author(s)

Henrik Bengtsson

The MultiArrayUnitModel class

Description

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.

Usage

MultiArrayUnitModel(..., listOfPriors=NULL)
MultiArrayUnitModel(..., listOfPriors=NULL)

Arguments

`...`	Arguments passed to `UnitModel`.
`listOfPriors`	A `list` of priors to be used when fitting the model.

Fields and Methods

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

Author(s)

Henrik Bengtsson

The NormExpBackgroundCorrection class

Description

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.

Usage

NormExpBackgroundCorrection(..., method=c("rma", "saddle", "mle"))
NormExpBackgroundCorrection(..., method=c("rma", "saddle", "mle"))

Arguments

`...`	Arguments passed to the constructor of `LimmaBackgroundCorrection`.
`method`	The estimator used, cf. argument `normexp.method` of `backgroundCorrect` in limma for more details.

Fields and Methods

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 ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Author(s)

Henrik Bengtsson

The OpticalBackgroundCorrection class

Description

Package: aroma.affymetrix
Class OpticalBackgroundCorrection

Directly known subclasses:

public static class OpticalBackgroundCorrection
extends BackgroundCorrection

This class represents "optical" background adjustment.

Usage

OpticalBackgroundCorrection(..., minimum=1)
OpticalBackgroundCorrection(..., minimum=1)

Arguments

`...`	Arguments passed to the constructor of `ProbeLevelTransform`.
`minimum`	The minimum signal allowed after adjustment.

Fields and Methods

Methods:

	`process`	-

Methods inherited from BackgroundCorrection:
getParameters, process

Methods inherited from ProbeLevelTransform:
getRootPath

Methods inherited from Transform:
getOutputDataSet, getOutputFiles

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Author(s)

Ken Simpson

The ParameterCelFile class

Description

Package: aroma.affymetrix
Class 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.

Usage

ParameterCelFile(..., encodeFunction=NULL, decodeFunction=NULL)
ParameterCelFile(..., encodeFunction=NULL, decodeFunction=NULL)

Arguments

`...`	Arguments passed to `AffymetrixCelFile`.
`encodeFunction`	A `function` taking a single `list` structure as its argument.
`decodeFunction`	A `function` taking a single `list` structure as its argument.

Fields and Methods

Methods:

	`extractDataFrame`	-
	`extractMatrix`	-
	`readUnits`	-

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

File format

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.

Author(s)

Henrik Bengtsson

The ParameterCelSet class

Description

Package: aroma.affymetrix
Class ParameterCelSet

Directly known subclasses:
ChipEffectSet, CnChipEffectSet, ExonChipEffectSet, FirmaSet, SnpChipEffectSet

public static class ParameterCelSet
extends ParametersInterface

A ParameterCelSet object represents a set of ParameterCelFile:s.

Usage

ParameterCelSet(...)
ParameterCelSet(...)

Arguments

...

Arguments passed to AffymetrixCelSet.

Fields and Methods

Methods:

	`extractDataFrame`	-
	`extractMatrix`	-

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Methods inherited from AffymetrixFileSet:
as, as.AffymetrixFileSet, byPath, getDefaultFullName

Author(s)

Henrik Bengtsson

The ProbeAffinityFile class

Description

Package: aroma.affymetrix
Class 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.

Usage

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

`...`	Arguments passed to `ParameterCelFile`.
`probeModel`	The specific type of probe model.

Fields and Methods

Methods:

	`readUnits`	-

Methods inherited from ParameterCelFile:
extractDataFrame, extractMatrix, readUnits

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Author(s)

Henrik Bengtsson

The ProbeLevelModel class

Description

Package: aroma.affymetrix
Class ProbeLevelModel

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.

Usage

ProbeLevelModel(..., standardize=TRUE)
ProbeLevelModel(..., standardize=TRUE)

Arguments

`...`	Arguments passed to `MultiArrayUnitModel`.
`standardize`	If `TRUE`, chip-effect and probe-affinity estimates are rescaled such that the product of the probe affinities is one.

Details

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 $\phi_k$ for a unit group must be constrained such that $\prod_k \phi_k = 1$ , or equivalently if $\phi_k > 0$ , $\sum_k \log(\phi_k) = 0$ .

Note that the above probe-affinity constraint guarantees that the estimated chip effects across models are on the same scale.

Fields and Methods

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

Author(s)

Henrik Bengtsson

The ProbeLevelTransform class

Description

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.

Usage

ProbeLevelTransform(...)
ProbeLevelTransform(...)

Arguments

...

Arguments passed to the constructor of Transform.

Details

Subclasses must implement the process() method.

Fields and Methods

Methods:
No methods defined.

Methods inherited from Transform:
getOutputDataSet, getOutputFiles

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Author(s)

Henrik Bengtsson

The ProbeLevelTransform3 class

Description

Package: aroma.affymetrix
Class 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.

Usage

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)

Arguments

`dataSet`	A `AffymetrixCelSet`.
`...`	Arguments passed to the constructor of `ProbeLevelTransform`.
`unitsToFit`	The units from which the normalization curve should be estimated. If `NULL`, all are considered.
`typesToFit`	Types of probes to be used when fitting the model.
`unitsToUpdate`	The units to be updated. If `NULL`, all are considered.
`typesToUpdate`	Types of probes to be updated.
`shift`	An optional amount to shift data before fitting and updating.

Fields and Methods

Methods:
No methods defined.

Methods inherited from ProbeLevelTransform:
getRootPath

Methods inherited from Transform:
getOutputDataSet, getOutputFiles

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Author(s)

Henrik Bengtsson

The QualityAssessmentFile class

Description

Package: aroma.affymetrix
Class QualityAssessmentFile

Directly known subclasses:

public abstract static class QualityAssessmentFile
extends AffymetrixCelFile

This class represents probe-level QC information (residuals, weights, etc.)

Usage

QualityAssessmentFile(...)
QualityAssessmentFile(...)

Arguments

...

Arguments passed to AffymetrixCelFile.

Fields and Methods

Methods:

	`findUnitsTodo`	-

Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Author(s)

Ken Simpson

The QualityAssessmentModel class

Description

Package: aroma.affymetrix
Class QualityAssessmentModel

Object
~~|
~~+--QualityAssessmentModel

Directly known subclasses:

public static class QualityAssessmentModel
extends Object

Usage

QualityAssessmentModel(plm=NULL, tags="*", ...)
QualityAssessmentModel(plm=NULL, tags="*", ...)

Arguments

`plm`	A `ProbeLevelModel`.
`tags`	A `character` `vector` of tags.
`...`	Not used.

Fields and Methods

Methods:

	`getChipEffectSet`	-
	`getDataSet`	-
	`getFullName`	-
	`getName`	-
	`getPath`	-
	`getPlm`	-
	`getResiduals`	-
	`getTags`	-
	`getWeights`	-
	`nbrOfArrays`	-
	`plotNuse`	-
	`plotRle`	-

Author(s)

Ken Simpson, Henrik Bengtsson

The QualityAssessmentSet class

Description

Package: aroma.affymetrix
Class QualityAssessmentSet

Directly known subclasses:

public static class QualityAssessmentSet
extends AffymetrixCelSet

Usage

QualityAssessmentSet(...)
QualityAssessmentSet(...)

Arguments

...

Arguments passed to constructor of AffymetrixCelSet.

Fields and Methods

Methods:
No methods defined.

Methods inherited from AffymetrixFileSet:
as, as.AffymetrixFileSet, byPath, getDefaultFullName

Author(s)

Ken Simpson

The QuantileNormalization class

Description

Package: aroma.affymetrix
Class 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.

Usage

QuantileNormalization(..., subsetToUpdate=NULL, typesToUpdate=NULL,
  targetDistribution=NULL, subsetToAvg=subsetToUpdate, typesToAvg=typesToUpdate)
QuantileNormalization(..., subsetToUpdate=NULL, typesToUpdate=NULL,
  targetDistribution=NULL, subsetToAvg=subsetToUpdate, typesToAvg=typesToUpdate)

Arguments

`...`	Arguments passed to the constructor of `ProbeLevelTransform`.
`subsetToUpdate`	The probes to be updated. If `NULL`, all probes are updated.
`typesToUpdate`	Types of probes to be updated.
`targetDistribution`	A `numeric` `vector`. The empirical distribution to which all arrays should be normalized to.
`subsetToAvg`	The probes to calculate average empirical distribution over. If a single `numeric` in (0,1), then this fraction of all probes will be used. If `NULL`, all probes are considered.
`typesToAvg`	Types of probes to be used when calculating the average empirical distribution. If `"pm"` and `"mm"` only perfect-match and mismatch probes are used, respectively. If `"pmmm"` both types are used.

Fields and Methods

Methods:

	`process`	-

Methods inherited from ProbeLevelTransform:
getRootPath

Methods inherited from Transform:
getOutputDataSet, getOutputFiles

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Author(s)

Henrik Bengtsson

Examples

## 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)

The ReseqCrosstalkCalibration class

Description

Package: aroma.affymetrix
Class 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.

Usage

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)

Arguments

`dataSet`	An `AffymetrixCelSet`.
`...`	Arguments passed to the constructor of `ProbeLevelTransform`.
`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 `NULL`, all probes are considered.
`mergeGroups`	A `logical` ...
`flavor`	A `character` string specifying what algorithm is used to fit the crosstalk calibration.
`alpha`, `q`, `Q`	Additional arguments passed to `fitMultiDimensionalCone()`.

Fields and Methods

Methods:

	`process`	-

Methods inherited from ProbeLevelTransform:
getRootPath

Methods inherited from Transform:
getOutputDataSet, getOutputFiles

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Author(s)

Henrik Bengtsson

The ResidualFile class

Description

Package: aroma.affymetrix
Class ResidualFile

Directly known subclasses:

public abstract static class ResidualFile
extends ParameterCelFile

This class represents estimates of residuals in the probe-level models.

Usage

ResidualFile(..., probeModel=c("pm"))
ResidualFile(..., probeModel=c("pm"))

Arguments

`...`	Arguments passed to `ParameterCelFile`.
`probeModel`	The specific type of model, e.g. `"pm"`.

Fields and Methods

Methods:

	`findUnitsTodo`	-
	`getImage`	-
	`readUnits`	-
	`writeImage`	-

Methods inherited from ParameterCelFile:
extractDataFrame, extractMatrix, readUnits

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Author(s)

Ken Simpson, Henrik Bengtsson

The ResidualSet class

Description

Package: aroma.affymetrix
Class ResidualSet

Directly known subclasses:

public static class ResidualSet
extends ParametersInterface

This class represents probe-level residuals from probe-level models.

Usage

ResidualSet(..., probeModel=c("pm"))
ResidualSet(..., probeModel=c("pm"))

Arguments

`...`	Arguments passed to `AffymetrixCelSet`.
`probeModel`	The specific type of model, e.g. `"pm"`.

Fields and Methods

Methods:

	`findUnitsTodo`	-
	`getAverageFile`	-
	`getCellIndices`	-
	`readUnits`	-

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Methods inherited from AffymetrixFileSet:
as, as.AffymetrixFileSet, byPath, getDefaultFullName

Author(s)

Ken Simpson, Henrik Bengtsson

The RmaBackgroundCorrection class

Description

Package: aroma.affymetrix
Class RmaBackgroundCorrection

Directly known subclasses:

public static class RmaBackgroundCorrection
extends BackgroundCorrection

This class represents the RMA background adjustment function.

Usage

RmaBackgroundCorrection(..., addJitter=FALSE, jitterSd=0.2, seed=6022007)
RmaBackgroundCorrection(..., addJitter=FALSE, jitterSd=0.2, seed=6022007)

Arguments

`...`	Arguments passed to the constructor of `BackgroundCorrection`.
`addJitter`	If `TRUE`, Zero-mean gaussian noise is added to the signals before being background corrected.
`jitterSd`	Standard deviation of the jitter noise added.
`seed`	An (optional) `integer` specifying a temporary random seed to be used for generating the (optional) jitter. The random seed is set to its original state when done. If `NULL`, it is not set.

Details

Internally bg.adjust is used to background correct the probe signals. The default is to background correct PM signals only.

Fields and Methods

Methods:

	`process`	-

Methods inherited from BackgroundCorrection:
getParameters, process

Methods inherited from ProbeLevelTransform:
getRootPath

Methods inherited from Transform:
getOutputDataSet, getOutputFiles

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Jitter noise

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.

Author(s)

Ken Simpson, Henrik Bengtsson

The RmaCnPlm class

Description

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

Usage

RmaCnPlm(..., combineAlleles=FALSE)
RmaCnPlm(..., combineAlleles=FALSE)

Arguments

`...`	Arguments passed to `RmaSnpPlm`.
`combineAlleles`	If `FALSE`, allele A and allele B are treated separately, otherwise together.

Fields and Methods

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 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

Model

TO DO.

Author(s)

Henrik Bengtsson

The RmaPlm class

Description

Package: aroma.affymetrix
Class 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).

Usage

RmaPlm(..., flavor=c("affyPLM", "oligo"))
RmaPlm(..., flavor=c("affyPLM", "oligo"))

Arguments

`...`	Arguments passed to `ProbeLevelModel`.
`flavor`	A `character` string specifying what model fitting algorithm to be used. This makes it possible to get identical estimates as other packages.

Fields and Methods

Methods:
No methods defined.

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

Model

For a single unit group, the log-additive model of RMA is:

$log_2(y_{ik}) = \beta_i + \alpha_k + \varepsilon_{ik}$

where $\beta_i$ are the chip effects for arrays $i=1,...,I$ , and $\alpha_k$ are the probe affinities for probes $k=1,...,K$ . The $\varepsilon_{ik}$ are zero-mean noise with equal variance. The model is constrained such that $\sum_k{\alpha_k} = 0$ .

Note that all PLM classes must return parameters on the intensity scale. For this class that means that $\theta_i = 2^\beta_i$ and $\phi_k = 2^\alpha_k$ are returned.

Different flavors of model fitting

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.

Author(s)

Henrik Bengtsson, Ken Simpson

References

Irizarry et al. Summaries of Affymetrix GeneChip probe level data. NAR, 2003, 31, e15.

The RmaSnpPlm class

Description

Package: aroma.affymetrix
Class RmaSnpPlm

Directly known subclasses:
RmaCnPlm

public abstract static class RmaSnpPlm
extends SnpPlm

Usage

RmaSnpPlm(..., mergeStrands=FALSE)
RmaSnpPlm(..., mergeStrands=FALSE)

Arguments

`...`	Arguments passed to `RmaPlm`.
`mergeStrands`	If `TRUE`, the sense and the anti-sense strands are fitted together, otherwise separately.

Fields and Methods

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 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

Author(s)

Henrik Bengtsson

The ScaleNormalization class

Description

Package: aroma.affymetrix
Class 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.

Usage

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)

Arguments

`dataSet`	`AffymetrixCelSet` to be normalized.
`...`	Arguments passed to the constructor of `ProbeLevelTransform`.
`targetAvg`	A `numeric` value.
`subsetToUpdate`	The probes to be updated. If `NULL`, all probes are updated.
`typesToUpdate`	Types of probes to be updated.
`subsetToAvg`	The probes to calculate average signal over. If a single `numeric` in (0,1), then this fraction of all probes will be used. If `NULL`, all probes are considered.
`typesToAvg`	Types of probes to be used when calculating the average signal. If `"pm"` and `"mm"` only perfect-match and mismatch probes are used, respectively. If `"pmmm"` both types are used.
`shift`	Optional amount of shift if data before fitting/normalizing.

Fields and Methods

Methods:

	`process`	-

Methods inherited from ProbeLevelTransform:
getRootPath

Methods inherited from Transform:
getOutputDataSet, getOutputFiles

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Author(s)

Henrik Bengtsson

The ScaleNormalization3 class

Description

Package: aroma.affymetrix
Class 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.

Usage

ScaleNormalization3(..., targetAvg=4400)
ScaleNormalization3(..., targetAvg=4400)

Arguments

`...`	Arguments passed to the constructor of `ProbeLevelTransform3`.
`targetAvg`	A `numeric` value.

Fields and Methods

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 ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Author(s)

Henrik Bengtsson

The SingleArrayUnitModel class

Description

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.

Usage

SingleArrayUnitModel(...)
SingleArrayUnitModel(...)

Arguments

...

Arguments passed to UnitModel.

Fields and Methods

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

Author(s)

Henrik Bengtsson

The SmoothMultiarrayModel class

Description

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.

Usage

SmoothMultiarrayModel(..., typoOfWeights=c("none", "1/s2"), bandwidth=10000, tags="*")
SmoothMultiarrayModel(..., typoOfWeights=c("none", "1/s2"), bandwidth=10000, tags="*")

Arguments

`...`	Arguments passed to the constructor of `ChromosomalModel`.
`typoOfWeights`	A `character` string.
`bandwidth`	A single `numeric` specifying the smoothing bandwidth in units of nucleotides.
`tags`	A `character` `vector` of tags to be added.

Fields and Methods

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

Author(s)

Henrik Bengtsson

The SmoothRmaModel class

Description

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.

Usage

SmoothRmaModel(...)
SmoothRmaModel(...)

Arguments

...

Arguments passed to the constructor of SmoothMultiarrayModel.

Fields and Methods

Methods:
No methods defined.

Methods inherited from SmoothMultiarrayModel:
as.character, createOutputTuple, fitOneChromosome, getAsteriskTags, getBandwidth, getFitUnitGroupFunction, getOutputTuple, getRootPath, setBandwidth

Author(s)

Henrik Bengtsson

The SnpChipEffectFile class

Description

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.

Usage

SnpChipEffectFile(..., mergeStrands=FALSE)
SnpChipEffectFile(..., mergeStrands=FALSE)

Arguments

`...`	Arguments passed to `ChipEffectFile`.
`mergeStrands`	Specifies if the strands are merged or not for these estimates.

Fields and Methods

Methods:

	`extractTheta`	-
	`extractTotalAndFracB`	-
	`readUnits`	-

Methods inherited from ParameterCelFile:
extractDataFrame, extractMatrix, readUnits

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Author(s)

Henrik Bengtsson

The SnpChipEffectSet class

Description

Package: aroma.affymetrix
Class SnpChipEffectSet

Directly known subclasses:
CnChipEffectSet

public static class SnpChipEffectSet
extends ChipEffectSet

This class represents estimates of chip effects in the probe-level models.

Usage

SnpChipEffectSet(..., mergeStrands="byFirstFile")
SnpChipEffectSet(..., mergeStrands="byFirstFile")

Arguments

`...`	Arguments passed to `ChipEffectSet`.
`mergeStrands`	Specifies if the strands are merged or not for these estimates.

Fields and Methods

Methods:

	`extractAlleleSet`	-
	`extractSnpCnvQSet`	-
	`extractSnpQSet`	-
	`extractTheta`	-
	`extractTotalAndFreqB`	-
	`getAverageFile`	-
	`getMergeStrands`	-
	`setMergeStrands`	-

Methods inherited from ParameterCelSet:
extractDataFrame, extractMatrix

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Methods inherited from AffymetrixFileSet:
as, as.AffymetrixFileSet, byPath, getDefaultFullName

Author(s)

Henrik Bengtsson

The SnpInformation class

Description

Package: aroma.affymetrix
Class SnpInformation

Directly known subclasses:
DChipSnpInformation, UflSnpInformation

public abstract static class SnpInformation
extends FileCacheKeyInterface

Usage

SnpInformation(...)
SnpInformation(...)

Arguments

...

Arguments passed to GenericDataFile.

Fields and Methods

Methods:

	`byChipType`	-
	`getChipType`	-
	`getData`	-
	`getFragmentLengths`	-
	`getFragmentStarts`	-
	`getFragmentStops`	-
	`nbrOfEnzymes`	-
	`nbrOfUnits`	-
	`readDataFrame`	-

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Author(s)

Henrik Bengtsson

The SnpPlm interface class

Description

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 ProbeLevelModels specific to SNP arrays.

Usage

SnpPlm(...)
SnpPlm(...)

Arguments

...

Not used.

Methods

Methods:

	`getCellIndices`	-
	`getChipEffectSet`	-
	`getMergeStrands`	-
	`getProbeAffinityFile`	-
	`setMergeStrands`	-

Methods inherited from Interface:
extend, print, uses

Requirements

Classes inheriting from this Interface must provide the following fields:

mergeStrands: A logical value indicating if strands should be merged or not.

Author(s)

Henrik Bengtsson

Examples

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)

The SnpProbeAffinityFile class

Description

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.

Usage

SnpProbeAffinityFile(..., mergeStrands=FALSE)
SnpProbeAffinityFile(..., mergeStrands=FALSE)

Arguments

`...`	Arguments passed to `ProbeAffinityFile`.
`mergeStrands`	Specifies if the strands are merged or not for these estimates.

Fields and Methods

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 AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Author(s)

Henrik Bengtsson

The SpatialReporter class

Description

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.

Usage

SpatialReporter(..., reference=NULL)
SpatialReporter(..., reference=NULL)

Arguments

`...`	Arguments passed to `AffymetrixCelSetReporter`.
`reference`	An optional reference `AffymetrixCelFile`.

Fields and Methods

Methods:

	`addColorMap`	-
	`getColorMaps`	-
	`plotMargins`	-
	`process`	-
	`setColorMaps`	-

Methods inherited from AffymetrixCelSetReporter:
as.character, getChipType, getDataSet, getPath, nbrOfArrays

Methods inherited from AffymetrixFileSetReporter:
getFileSet, getInputName, getInputTags

Author(s)

Henrik Bengtsson

The TransformReport class

Description

Package: aroma.affymetrix
Class TransformReport

Object
~~|
~~+--TransformReport

Directly known subclasses:

public static class TransformReport
extends Object

Usage

TransformReport(inSet=NULL, outSet=NULL, ...)
TransformReport(inSet=NULL, outSet=NULL, ...)

Arguments

`inSet`	The input data set as an `AffymetrixCelSet`.
`outSet`	The output data set as an `AffymetrixCelSet`.
`...`	Not used.

Fields and Methods

Methods:

	`getCdf`	-
	`getFullName`	-
	`getInputDataSet`	-
	`getName`	-
	`getOutputDataSet`	-
	`getPath`	-
	`getTags`	-
	`getUnitNamesFile`	-
	`getUnitTypesFile`	-
	`getYY`	-
	`nbrOfArrays`	-
	`plotXYCurve`	-
	`plotXYCurveLog2`	-
	`seq`	-
	`writeImageCombined`	-
	`writeImages`	-

Author(s)

Henrik Bengtsson

The UgpGenomeInformation class

Description

Package: aroma.affymetrix
Class UgpGenomeInformation

Directly known subclasses:

public abstract static class UgpGenomeInformation
extends GenomeInformation

This class represents Aroma UGP genome information files.

Usage

UgpGenomeInformation(..., .ugp=NULL, .verify=TRUE)
UgpGenomeInformation(..., .ugp=NULL, .verify=TRUE)

Arguments

`...`	Arguments passed to `GenomeInformation`.
`.ugp`	For internal use only.
`.verify`	For internal use only.

Fields and Methods

Methods:

	`byChipType`	-
	`getChipType`	-
	`getChromosomes`	-
	`getData`	-
	`getUnitsOnChromosome`	-
	`isCompatibleWithCdf`	-
	`nbrOfUnits`	-
	`readDataFrame`	-

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Author(s)

Henrik Bengtsson

The UnitModel class

Description

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.

Usage

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, ...)

Arguments

`dataSet`	An `AffymetrixCelSet` to which this model should be fitted.
`probeModel`	A `character` string specifying how PM and MM values should be modeled. By default only PM signals are used.
`shift`	An optional amount the signals should be shifted (translated) before fitting the model.
`...`	Arguments passed to the constructor of `Model`.

Fields and Methods

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

Author(s)

Henrik Bengtsson

The UnitTypeScaleNormalization class

Description

Package: aroma.affymetrix
Class 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.

Usage

UnitTypeScaleNormalization(..., targetAvg=4400)
UnitTypeScaleNormalization(..., targetAvg=4400)

Arguments

`...`	Arguments passed to the constructor of `ProbeLevelTransform3`.
`targetAvg`	A `numeric` value.

Fields and Methods

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 ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Author(s)

Henrik Bengtsson

The WeightsFile class

Description

Package: aroma.affymetrix
Class WeightsFile

Directly known subclasses:

public abstract static class WeightsFile
extends ParameterCelFile

This class represents weights calculated from residuals of probe-level models.

Usage

WeightsFile(..., probeModel=c("pm"))
WeightsFile(..., probeModel=c("pm"))

Arguments

`...`	Arguments passed to `ParameterCelFile`.
`probeModel`	The specific type of model, e.g. `"pm"`.

Fields and Methods

Methods:

	`findUnitsTodo`	-
	`getImage`	-
	`readUnits`	-
	`writeImage`	-

Methods inherited from ParameterCelFile:
extractDataFrame, extractMatrix, readUnits

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Methods inherited from AromaMicroarrayDataFile:
getAttributeXY, getChipType, getPlatform, getPloidy, getXAM, hasAttributeXY, isAverageFile, setAttributeXY, setAttributesByTags

Methods inherited from FileCacheKeyInterface:
getCacheKey

Methods inherited from CacheKeyInterface:
getCacheKey

Author(s)

Henrik Bengtsson, Ken Simpson

The WeightsSet class

Description

Package: aroma.affymetrix
Class WeightsSet

Directly known subclasses:

public static class WeightsSet
extends ParametersInterface

This class represents probe-level weights.

Usage

WeightsSet(..., probeModel=c("pm"))
WeightsSet(..., probeModel=c("pm"))

Arguments

`...`	Arguments passed to `AffymetrixCelSet`.
`probeModel`	The specific type of model, e.g. `"pm"`.

Fields and Methods

Methods:

	`findUnitsTodo`	-
	`getAverageFile`	-
	`getCellIndices`	-
	`readUnits`	-

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Methods inherited from AffymetrixFileSet:
as, as.AffymetrixFileSet, byPath, getDefaultFullName

Author(s)

Henrik Bengtsson, Ken Simpson

Package 'aroma.affymetrix'

Help Index