Title: | Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework |
---|---|
Description: | Core methods and classes used by higher-level 'aroma.*' packages part of the Aroma Project, e.g. 'aroma.affymetrix' and 'aroma.cn'. |
Authors: | Henrik Bengtsson [aut, cre, cph], Mark Robinson [ctb], Ken Simpson [ctb] |
Maintainer: | Henrik Bengtsson <[email protected]> |
License: | LGPL (>= 2.1) |
Version: | 3.3.0 |
Built: | 2024-08-13 04:19:09 UTC |
Source: | https://github.com/HenrikBengtsson/aroma.core |
Core methods and classes used by higher-level 'aroma.*' packages part of the Aroma Project, e.g. 'aroma.affymetrix' and 'aroma.cn'.
This package is a support package for aroma.affymetrix. This package should be considered to be in an alpha or beta phase. You should expect the API to be changing over time. For practical purposes, consider this package a private package.
This package is available on CRAN, i.e. to install do
install.packages("aroma.core")
.
The releases of this package is licensed under LGPL version 2.1 or newer.
The development code of the packages is under a private licence (where applicable) and patches sent to the author fall under the latter license, but will be, if incorporated, released under the "release" license above.
Henrik Bengtsson
[1] 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. http://www.ci.tuwien.ac.at/Conferences/DSC-2003/Proceedings/
Package: aroma.core
Class AbstractCNData
data.frame
~~|
~~+--
RichDataFrame
~~~~~~~|
~~~~~~~+--
RawGenomicSignals
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
AbstractCNData
Directly known subclasses:
AbstractPSCNData, NonPairedPSCNData, PairedPSCNData
public class AbstractCNData
extends RawGenomicSignals
An AbstractCNData object holds copy number data.
AbstractCNData(chromosome=NULL, x=NULL, y=NULL, ..., name=NULL, .virtuals=NULL)
AbstractCNData(chromosome=NULL, x=NULL, y=NULL, ..., name=NULL, .virtuals=NULL)
chromosome |
(Optional) An |
x |
Optional |
y |
|
... |
Optional named locus-specific signal |
name |
Optional |
.virtuals |
Methods:
findLargeGaps |
- | |
getChipType |
- | |
getLocusData |
- | |
getPlatform |
- | |
setChipType |
- | |
setPlatform |
- | |
Methods inherited from RawGenomicSignals:
*, +, -, addBy, append, applyBinaryOperator, as.character, as.data.frame, assertOneChromosome, binnedSmoothing, binnedSmoothingByField, clearCache, clone, divideBy, drawDensity, estimateStandardDeviation, extractChromosome, extractChromosomes, extractDataForSegmentation, extractRegion, extractRegions, extractSubset, gaussianSmoothing, getBasicField, getCXY, getChromosome, getChromosomes, getDefaultLocusFields, getLocusFields, getPositions, getSigma, getSignalColumnName, getSignalColumnNames, getSignals, getWeights, getXScale, getXY, getYScale, hasWeights, kernelSmoothing, lines, multiplyBy, nbrOfChromosomes, nbrOfLoci, plot, points, print, segmentByCBS, segmentByGLAD, segmentByHaarSeg, segmentByMPCBS, setBasicField, setSigma, setSignals, setWeights, setXScale, setYScale, signalRange, sort, subtractBy, xMax, xMin, xRange, xSeq, yMax, yMin, yRange
Methods inherited from RichDataFrame:
$, $<-, [, [[, [[<-, as.data.frame, as.list, dim, dropVirtualColumn, getColumnNames, getColumnNamesTranslator, getFullName, getName, getTags, getVirtualColumn, getVirtualColumnFunction, getVirtualColumnNames, hasColumn, hasColumns, hasVirtualColumn, hasVirtualColumns, length, names, newInstance, print, rbind, setAttributes, setColumnNamesMap, setColumnNamesTranslator, setName, setTags, setVirtualColumn, subset, translateColumnNames
Methods inherited from data.frame:
$<-,data.frame-method, $<-, Math, Ops,nonStructure,vector-method, Ops,structure,vector-method, Ops,vector,nonStructure-method, Ops,vector,structure-method, Ops, Summary, [, [<-,data.frame-method, [<-, [[, [[<-,data.frame-method, [[<-, aggregate, anyDuplicated, anyNA, as.NonPairedPSCNData, as.PairedPSCNData, as.data.frame, as.list, as.matrix, as.vector, attachLocally, by, callSegmentationOutliers, cbind, coerce,ANY,list-method, coerce,oldClass,S3-method, dim, dimnames, dimnames<-, dropSegmentationOutliers, droplevels, duplicated, edit, findLargeGaps, format, formula, head, initialize,oldClass-method, is.na, merge, na.exclude, na.omit, plot, print, prompt, rbind, row.names, row.names<-, rowsum, segmentByCBS, segmentByPairedPSCBS, show,oldClass-method, slotsFromS3,data.frame-method, split, split<-, stack, str, subset, summary, t, tail, transform, type.convert, unique, unstack, unwrap, within, wrap, writeDataFrame, xtfrm
Henrik Bengtsson
Package: aroma.core
Class AbstractPSCNData
data.frame
~~|
~~+--
RichDataFrame
~~~~~~~|
~~~~~~~+--
RawGenomicSignals
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
AbstractCNData
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
AbstractPSCNData
Directly known subclasses:
NonPairedPSCNData, PairedPSCNData
public class AbstractPSCNData
extends AbstractCNData
A AbstractPSCNData object holds parent-specific copy number data.
AbstractPSCNData(chromosome=NULL, x=NULL, isSNP=NULL, mu=NULL, ...)
AbstractPSCNData(chromosome=NULL, x=NULL, isSNP=NULL, mu=NULL, ...)
chromosome |
(Optional) An |
x |
Optional |
isSNP |
An optional |
mu |
An optional |
... |
Optional named locus-specific signal |
Methods:
No methods defined.
Methods inherited from AbstractCNData:
findLargeGaps, getChipType, getLocusData, getPlatform, hasKnownPositions, orderAlongGenome, setChipType, setPlatform
Methods inherited from RawGenomicSignals:
*, +, -, addBy, append, applyBinaryOperator, as.character, as.data.frame, assertOneChromosome, binnedSmoothing, binnedSmoothingByField, clearCache, clone, divideBy, drawDensity, estimateStandardDeviation, extractChromosome, extractChromosomes, extractDataForSegmentation, extractRegion, extractRegions, extractSubset, gaussianSmoothing, getBasicField, getCXY, getChromosome, getChromosomes, getDefaultLocusFields, getLocusFields, getPositions, getSigma, getSignalColumnName, getSignalColumnNames, getSignals, getWeights, getXScale, getXY, getYScale, hasWeights, kernelSmoothing, lines, multiplyBy, nbrOfChromosomes, nbrOfLoci, plot, points, print, segmentByCBS, segmentByGLAD, segmentByHaarSeg, segmentByMPCBS, setBasicField, setSigma, setSignals, setWeights, setXScale, setYScale, signalRange, sort, subtractBy, xMax, xMin, xRange, xSeq, yMax, yMin, yRange
Methods inherited from RichDataFrame:
$, $<-, [, [[, [[<-, as.data.frame, as.list, dim, dropVirtualColumn, getColumnNames, getColumnNamesTranslator, getFullName, getName, getTags, getVirtualColumn, getVirtualColumnFunction, getVirtualColumnNames, hasColumn, hasColumns, hasVirtualColumn, hasVirtualColumns, length, names, newInstance, print, rbind, setAttributes, setColumnNamesMap, setColumnNamesTranslator, setName, setTags, setVirtualColumn, subset, translateColumnNames
Methods inherited from data.frame:
$<-,data.frame-method, $<-, Math, Ops,nonStructure,vector-method, Ops,structure,vector-method, Ops,vector,nonStructure-method, Ops,vector,structure-method, Ops, Summary, [, [<-,data.frame-method, [<-, [[, [[<-,data.frame-method, [[<-, aggregate, anyDuplicated, anyNA, as.NonPairedPSCNData, as.PairedPSCNData, as.data.frame, as.list, as.matrix, as.vector, attachLocally, by, callSegmentationOutliers, cbind, coerce,ANY,list-method, coerce,oldClass,S3-method, dim, dimnames, dimnames<-, dropSegmentationOutliers, droplevels, duplicated, edit, findLargeGaps, format, formula, head, initialize,oldClass-method, is.na, merge, na.exclude, na.omit, plot, print, prompt, rbind, row.names, row.names<-, rowsum, segmentByCBS, segmentByPairedPSCBS, show,oldClass-method, slotsFromS3,data.frame-method, split, split<-, stack, str, subset, summary, t, tail, transform, type.convert, unique, unstack, unwrap, within, wrap, writeDataFrame, xtfrm
Henrik Bengtsson
A binary file holding local CpG density for each cell (probe/feature).
AromaCellCpgFile(...)
AromaCellCpgFile(...)
... |
Arguments passed to constructor of
|
Note that this class does not assume a rectangular chip layout. In other words, there is no concept of mapping a spatial location on the array to a cell index and vice versa. The reason for this to be able to use this class also for non-rectangular chip types.
Mark Robinson
A binary file holding chromosome/position for each cell.
AromaCellPositionFile(...)
AromaCellPositionFile(...)
... |
Arguments passed to constructor of
|
Note that this class does not assume a rectangular chip layout. In other words, there is no concept of mapping a spatial location on the array to a cell index and vice versa. The reason for this to be able to use this class also for non-rectangular chip types.
Henrik Bengtsson
Package: aroma.core
Class AromaCellTabularBinaryFile
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
ColumnNamesInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
GenericTabularFile
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
CacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaTabularBinaryFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaMicroarrayTabularBinaryFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaCellTabularBinaryFile
Directly known subclasses:
AromaCellCpgFile, AromaCellPositionFile, AromaCellSequenceFile
public abstract static class AromaCellTabularBinaryFile
extends AromaMicroarrayTabularBinaryFile
An AromaCellTabularBinaryFile is an AromaTabularBinaryFile
with
the constraint that the rows map one-to-one to the cells (features)
of a microarray.
AromaCellTabularBinaryFile(...)
AromaCellTabularBinaryFile(...)
... |
Arguments passed to |
Methods:
byChipType |
- | |
nbrOfCells |
- | |
Methods inherited from AromaMicroarrayTabularBinaryFile:
allocate, as.character, byChipType, findByChipType, getChipType, getFilenameExtension, getPlatform
Methods inherited from AromaPlatformInterface:
getAromaPlatform, getAromaUflFile, getAromaUgpFile, getChipType, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith
Methods inherited from AromaTabularBinaryFile:
[, [<-, [[, allocate, as.character, colApply, colMeans, colStats, colSums, dimnames<-, getBytesPerColumn, getColClasses, getDefaultColumnNames, getRootName, importFrom, nbrOfColumns, nbrOfRows, readColumns, readDataFrame, readFooter, readHeader, readRawFooter, setAttributesByTags, subset, summary, updateData, updateDataColumn, writeFooter, writeRawFooter
Methods inherited from FileCacheKeyInterface:
getCacheKey
Methods inherited from CacheKeyInterface:
getCacheKey
Methods inherited from GenericTabularFile:
[, as.character, dim, extractMatrix, head, nbrOfColumns, nbrOfRows, readColumns, readDataFrame, tail, writeColumnsToFiles
Methods inherited from ColumnNamesInterface:
appendColumnNamesTranslator, appendColumnNamesTranslatorByNULL, appendColumnNamesTranslatorBycharacter, appendColumnNamesTranslatorByfunction, appendColumnNamesTranslatorBylist, clearColumnNamesTranslator, clearListOfColumnNamesTranslators, getColumnNames, getColumnNamesTranslator, getDefaultColumnNames, getListOfColumnNamesTranslators, nbrOfColumns, setColumnNames, setColumnNamesTranslator, setListOfColumnNamesTranslators, updateColumnNames
Methods inherited from GenericDataFile:
as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.core
Class AromaGenomeTextFile
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
ColumnNamesInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
GenericTabularFile
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
TabularTextFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
CacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaGenomeTextFile
Directly known subclasses:
AromaUcscGenomeTextFile
public abstract static class AromaGenomeTextFile
extends FileCacheKeyInterface
An AromaGenomeTextFile represents a annotation tabular text file that specifies the number of bases (nucleotides) per chromosome for a particular genome/organism.
AromaGenomeTextFile(...)
AromaGenomeTextFile(...)
... |
Arguments passed to |
An AromaGenomeTextFile is a tab-delimited text file with a header containing (at least) column names 'chromosome' and 'nbrOfBases'. The 'chromosome' column specifies the chromosomes (character strings) and the 'nbrOfBases' column specifies the lengths (integer) of the chromosomes in number of bases (nucleotides).
The filename of an AromaGenomeTextFile should have format "<genome>,chromosomes(,<tag>)*.txt", and be located in annotationData/genomes/<genome>/, e.g. annotationData/genomes/Human/Human,chromosomes,max,20090503.txt.
Methods:
byGenome |
- | |
readDataFrame |
- | |
Methods inherited from FileCacheKeyInterface:
getCacheKey
Methods inherited from CacheKeyInterface:
getCacheKey
Methods inherited from TabularTextFile:
as.character, getCommentChar, getDefaultColumnClassPatterns, getDefaultColumnClasses, getDefaultColumnNames, getHeader, getReadArguments, hasColumnHeader, nbrOfLines, nbrOfRows, readColumnNames, readColumns, readDataFrame, readLines, readRawHeader, setCommentChar
Methods inherited from GenericTabularFile:
[, as.character, dim, extractMatrix, head, nbrOfColumns, nbrOfRows, readColumns, readDataFrame, tail, writeColumnsToFiles
Methods inherited from ColumnNamesInterface:
appendColumnNamesTranslator, appendColumnNamesTranslatorByNULL, appendColumnNamesTranslatorBycharacter, appendColumnNamesTranslatorByfunction, appendColumnNamesTranslatorBylist, clearColumnNamesTranslator, clearListOfColumnNamesTranslators, getColumnNames, getColumnNamesTranslator, getDefaultColumnNames, getListOfColumnNamesTranslators, nbrOfColumns, setColumnNames, setColumnNamesTranslator, setListOfColumnNamesTranslators, updateColumnNames
Methods inherited from GenericDataFile:
as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
# Locate a Human,chromosomes(,.*)*.txt file db <- AromaGenomeTextFile$byGenome("Human") print(db) # Read the data df <- readDataFrame(db) print(df) str(df) # Details on the file format oopts <- options(width=40) print(readLines(db)) options(oopts)
# Locate a Human,chromosomes(,.*)*.txt file db <- AromaGenomeTextFile$byGenome("Human") print(db) # Read the data df <- readDataFrame(db) print(df) str(df) # Details on the file format oopts <- options(width=40) print(readLines(db)) options(oopts)
Package: aroma.core
Class AromaMicroarrayDataFile
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
CacheKeyInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
AromaMicroarrayDataFile
Directly known subclasses:
public abstract static class AromaMicroarrayDataFile
extends FileCacheKeyInterface
An AromaMicroarrayDataFile object represents a single microarray data file. Each such file originates from a specific chip type on a given platform.
AromaMicroarrayDataFile(...)
AromaMicroarrayDataFile(...)
... |
Arguments passed to |
Methods:
getChipType |
- | |
getPlatform |
- | |
isAverageFile |
- | |
Methods inherited from FileCacheKeyInterface:
getCacheKey
Methods inherited from CacheKeyInterface:
getCacheKey
Methods inherited from GenericDataFile:
as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
An object of this class is typically part of an
AromaMicroarrayDataSet
.
Package: aroma.core
Class AromaMicroarrayDataSet
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFileSet
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
AromaMicroarrayDataSet
Directly known subclasses:
public abstract static class AromaMicroarrayDataSet
extends GenericDataFileSet
An AromaMicroarrayDataSet object represents a set of
AromaMicroarrayDataFile
s with identical chip types.
AromaMicroarrayDataSet(files=NULL, ...)
AromaMicroarrayDataSet(files=NULL, ...)
files |
A |
... |
Arguments passed to |
Methods:
as.AromaMicroarrayDataSetList |
- | |
as.AromaMicroarrayDataSetTuple |
- | |
getAverageFile |
- | |
getChipType |
- | |
getPlatform |
- | |
Methods inherited from GenericDataFileSet:
[, [[, anyDuplicated, anyNA, append, appendFiles, appendFullNamesTranslator, appendFullNamesTranslatorByNULL, appendFullNamesTranslatorByTabularTextFile, appendFullNamesTranslatorByTabularTextFileSet, appendFullNamesTranslatorBydata.frame, appendFullNamesTranslatorByfunction, appendFullNamesTranslatorBylist, as.character, as.list, byName, byPath, c, clearCache, clearFullNamesTranslator, clone, copyTo, dsApplyInPairs, duplicated, equals, extract, findByName, findDuplicated, getChecksum, getChecksumFileSet, getChecksumObjects, getDefaultFullName, getFile, getFileClass, getFileSize, getFiles, getFullNames, getNames, getOneFile, getPath, getPathnames, getSubdirs, gunzip, gzip, hasFile, indexOf, is.na, names, nbrOfFiles, rep, resetFullNames, setFullNamesTranslator, sortBy, unique, update2, updateFullName, updateFullNames, validate, getFullNameTranslatorSet, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.core
Class AromaMicroarrayDataSetTuple
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFileSetList
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
AromaMicroarrayDataSetTuple
Directly known subclasses:
AromaUnitTotalCnBinarySetTuple
public abstract static class AromaMicroarrayDataSetTuple
extends GenericDataFileSetList
AromaMicroarrayDataSetTuple(..., .setClass="AromaMicroarrayDataSet")
AromaMicroarrayDataSetTuple(..., .setClass="AromaMicroarrayDataSet")
... |
Arguments passed to |
.setClass |
The name of the class of the input set. |
Methods:
as |
- | |
as.AromaMicroarrayDataSetTuple |
- | |
getChipTypes |
- | |
getFullNames |
- | |
getSets |
- | |
getTags |
- | |
nbrOfChipTypes |
Gets the number of chip types. | |
Methods inherited from GenericDataFileSetList:
as, as.GenericDataFileSetList, as.character, as.data.frame, as.list, assertDuplicates, clone, extract, getAsteriskTags, getDefaultFullName, getFileList, getFileListClass, getFullNames, getNames, getSet, getSets, getTags, indexOf, length, nbrOfFiles, nbrOfSets, setTags
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.core
Class AromaMicroarrayTabularBinaryFile
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
ColumnNamesInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
GenericTabularFile
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
CacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaTabularBinaryFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaMicroarrayTabularBinaryFile
Directly known subclasses:
AromaCellCpgFile, AromaCellPositionFile, AromaCellSequenceFile, AromaCellTabularBinaryFile, AromaUflFile, AromaUgcFile, AromaUgpFile, AromaUnitChromosomeTabularBinaryFile, AromaUnitGcContentFile, AromaUnitTabularBinaryFile
public abstract static class AromaMicroarrayTabularBinaryFile
extends AromaPlatformInterface
An AromaMicroarrayTabularBinaryFile is an abstract
AromaTabularBinaryFile
.
AromaMicroarrayTabularBinaryFile(...)
AromaMicroarrayTabularBinaryFile(...)
... |
Arguments passed to |
Methods:
byChipType |
- | |
getChipType |
- | |
getFilenameExtension |
- | |
getPlatform |
- | |
Methods inherited from AromaPlatformInterface:
getAromaPlatform, getAromaUflFile, getAromaUgpFile, getChipType, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith
Methods inherited from AromaTabularBinaryFile:
[, [<-, [[, allocate, as.character, colApply, colMeans, colStats, colSums, dimnames<-, getBytesPerColumn, getColClasses, getDefaultColumnNames, getRootName, importFrom, nbrOfColumns, nbrOfRows, readColumns, readDataFrame, readFooter, readHeader, readRawFooter, setAttributesByTags, subset, summary, updateData, updateDataColumn, writeFooter, writeRawFooter
Methods inherited from FileCacheKeyInterface:
getCacheKey
Methods inherited from CacheKeyInterface:
getCacheKey
Methods inherited from GenericTabularFile:
[, as.character, dim, extractMatrix, head, nbrOfColumns, nbrOfRows, readColumns, readDataFrame, tail, writeColumnsToFiles
Methods inherited from ColumnNamesInterface:
appendColumnNamesTranslator, appendColumnNamesTranslatorByNULL, appendColumnNamesTranslatorBycharacter, appendColumnNamesTranslatorByfunction, appendColumnNamesTranslatorBylist, clearColumnNamesTranslator, clearListOfColumnNamesTranslators, getColumnNames, getColumnNamesTranslator, getDefaultColumnNames, getListOfColumnNamesTranslators, nbrOfColumns, setColumnNames, setColumnNamesTranslator, setListOfColumnNamesTranslators, updateColumnNames
Methods inherited from GenericDataFile:
as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.core
Class AromaPlatform
Object
~~|
~~+--
AromaPlatform
Directly known subclasses:
public abstract static class AromaPlatform
extends Object
An AromaPlatform provides methods for a given platform, e.g. Affymetrix, Agilent, Illumina.
AromaPlatform(...)
AromaPlatform(...)
... |
Not used. |
Methods:
byName |
- | |
equals |
- | |
getAromaUgpFile |
- | |
getName |
- | |
getUnitNamesFile |
- | |
getUnitTypesFile |
- | |
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
## Not run: library("aroma.affymetrix") platform <- AromaPlatform$byName("Affymetrix") print(platform) stopifnot(getName(platform) == "Affymetrix") ## End(Not run)
## Not run: library("aroma.affymetrix") platform <- AromaPlatform$byName("Affymetrix") print(platform) stopifnot(getName(platform) == "Affymetrix") ## End(Not run)
Package: aroma.core
Class AromaPlatformInterface
Interface
~~|
~~+--
AromaPlatformInterface
Directly known subclasses:
AromaCellCpgFile, AromaCellPositionFile, AromaCellSequenceFile, AromaCellTabularBinaryFile, AromaMicroarrayTabularBinaryFile, AromaUflFile, AromaUgcFile, AromaUgpFile, AromaUnitCallFile, AromaUnitChromosomeTabularBinaryFile, AromaUnitFracBCnBinaryFile, AromaUnitGcContentFile, AromaUnitGenotypeCallFile, AromaUnitPscnBinaryFile, AromaUnitSignalBinaryFile, AromaUnitTabularBinaryFile, AromaUnitTotalCnBinaryFile, AromaUnitTypesFile
public abstract class AromaPlatformInterface
extends Interface
An AromaPlatformInterface provides methods for a given platform, e.g. Affymetrix, Agilent, Illumina.
AromaPlatformInterface(...)
AromaPlatformInterface(...)
... |
Not used. |
Methods:
getAromaPlatform |
Gets the platform. | |
getAromaUflFile |
- | |
getAromaUgpFile |
- | |
getChipType |
Gets the chip type. | |
getPlatform |
Gets the platform. | |
getUnitNamesFile |
- | |
getUnitTypesFile |
- | |
Methods inherited from Interface:
extend, print, uses
Henrik Bengtsson
Package: aroma.core
Class AromaRepository
Object
~~|
~~+--
AromaRepository
Directly known subclasses:
public static class AromaRepository
extends Object
An AromaRepository object provides methods for downloading annotation data from the Aroma repository.
AromaRepository(urlPath="https://www.aroma-project.org/data", verbose=FALSE, ...)
AromaRepository(urlPath="https://www.aroma-project.org/data", verbose=FALSE, ...)
urlPath |
The URL to the Aroma repository. |
verbose |
The |
... |
Not used. |
Methods:
downloadACC |
- | |
downloadACM |
- | |
downloadACP |
- | |
downloadACS |
- | |
downloadAll |
- | |
downloadCDF |
- | |
downloadChipTypeFile |
Download a particular chip type annotation file. | |
downloadProbeSeqsTXT |
- | |
downloadTXT |
- | |
downloadUFL |
- | |
downloadUGC |
- | |
downloadUGP |
- | |
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.core
Class AromaTabularBinaryFile
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
ColumnNamesInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
GenericTabularFile
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
CacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaTabularBinaryFile
Directly known subclasses:
AromaCellCpgFile, AromaCellPositionFile, AromaCellSequenceFile, AromaCellTabularBinaryFile, AromaMicroarrayTabularBinaryFile, AromaUflFile, AromaUgcFile, AromaUgpFile, AromaUnitCallFile, AromaUnitChromosomeTabularBinaryFile, AromaUnitFracBCnBinaryFile, AromaUnitGcContentFile, AromaUnitGenotypeCallFile, AromaUnitPscnBinaryFile, AromaUnitSignalBinaryFile, AromaUnitTabularBinaryFile, AromaUnitTotalCnBinaryFile, AromaUnitTypesFile
public abstract static class AromaTabularBinaryFile
extends FileCacheKeyInterface
A AromaTabularBinaryFile represents a file with a binary format. It has a well defined header, a data section, and a footer.
AromaTabularBinaryFile(...)
AromaTabularBinaryFile(...)
... |
Arguments passed to |
Methods:
[ |
- | |
[<- |
- | |
colMeans |
- | |
colSums |
- | |
getBytesPerColumn |
- | |
getColClasses |
- | |
importFrom |
- | |
nbrOfColumns |
- | |
nbrOfRows |
- | |
readColumns |
- | |
readFooter |
Reads the file footer in XML format into a named nested list. | |
subset |
- | |
summary |
- | |
writeFooter |
Writes a named nested list to the file footer in XML format. | |
Methods inherited from FileCacheKeyInterface:
getCacheKey
Methods inherited from CacheKeyInterface:
getCacheKey
Methods inherited from GenericTabularFile:
[, as.character, dim, extractMatrix, head, nbrOfColumns, nbrOfRows, readColumns, readDataFrame, tail, writeColumnsToFiles
Methods inherited from ColumnNamesInterface:
appendColumnNamesTranslator, appendColumnNamesTranslatorByNULL, appendColumnNamesTranslatorBycharacter, appendColumnNamesTranslatorByfunction, appendColumnNamesTranslatorBylist, clearColumnNamesTranslator, clearListOfColumnNamesTranslators, getColumnNames, getColumnNamesTranslator, getDefaultColumnNames, getListOfColumnNamesTranslators, nbrOfColumns, setColumnNames, setColumnNamesTranslator, setListOfColumnNamesTranslators, updateColumnNames
Methods inherited from GenericDataFile:
as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.core
Class AromaTabularBinarySet
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFileSet
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
GenericTabularFileSet
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
AromaTabularBinarySet
Directly known subclasses:
AromaUnitCallSet, AromaUnitFracBCnBinarySet, AromaUnitGenotypeCallSet, AromaUnitPscnBinarySet, AromaUnitSignalBinarySet, AromaUnitTotalCnBinarySet
public static class AromaTabularBinarySet
extends GenericTabularFileSet
An AromaTabularBinarySet object represents a set of
AromaTabularBinaryFile
s with identical chip types.
AromaTabularBinarySet(files=NULL, ...)
AromaTabularBinarySet(files=NULL, ...)
files |
A |
... |
Arguments passed to |
Methods:
No methods defined.
Methods inherited from GenericTabularFileSet:
extractMatrix, calculateAverageColumnAcrossFiles
Methods inherited from GenericDataFileSet:
[, [[, anyDuplicated, anyNA, append, appendFiles, appendFullNamesTranslator, appendFullNamesTranslatorByNULL, appendFullNamesTranslatorByTabularTextFile, appendFullNamesTranslatorByTabularTextFileSet, appendFullNamesTranslatorBydata.frame, appendFullNamesTranslatorByfunction, appendFullNamesTranslatorBylist, as.character, as.list, byName, byPath, c, clearCache, clearFullNamesTranslator, clone, copyTo, dsApplyInPairs, duplicated, equals, extract, findByName, findDuplicated, getChecksum, getChecksumFileSet, getChecksumObjects, getDefaultFullName, getFile, getFileClass, getFileSize, getFiles, getFullNames, getNames, getOneFile, getPath, getPathnames, getSubdirs, gunzip, gzip, hasFile, indexOf, is.na, names, nbrOfFiles, rep, resetFullNames, setFullNamesTranslator, sortBy, unique, update2, updateFullName, updateFullNames, validate, getFullNameTranslatorSet, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.core
Class AromaTransform
Object
~~|
~~+--
ParametersInterface
~~~~~~~|
~~~~~~~+--
AromaTransform
Directly known subclasses:
public abstract static class AromaTransform
extends ParametersInterface
This abstract class represents a transform (algorithm/operator) that transforms data. A transform has an input data set, which is transformed into an output data set.
AromaTransform(dataSet=NULL, tags="*", ..., .reqSetClass="AromaMicroarrayDataSet")
AromaTransform(dataSet=NULL, tags="*", ..., .reqSetClass="AromaMicroarrayDataSet")
dataSet |
The input data set as an |
tags |
A |
... |
Not used. |
.reqSetClass |
Internal argument. |
Subclasses must implement the process()
method.
Methods:
getFullName |
Gets the full name of the output data set. | |
getInputDataSet |
Gets the input data set. | |
getName |
Gets the name of the output data set. | |
getOutputDataSet |
Gets the transformed data set. | |
getPath |
Gets the path of the output directory. | |
getRootPath |
Gets the root path of the output directory. | |
getTags |
Gets the tags of the output data set. | |
isDone |
Checks if the data set is processed or not. | |
process |
Processes the data set. | |
setTags |
- | |
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.core
Class AromaUnitCallFile
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
ColumnNamesInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
GenericTabularFile
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
CacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaTabularBinaryFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaUnitSignalBinaryFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaUnitCallFile
Directly known subclasses:
AromaUnitGenotypeCallFile
public static class AromaUnitCallFile
extends AromaUnitSignalBinaryFile
An AromaUnitCallFile is a AromaUnitSignalBinaryFile
.
AromaUnitCallFile(...)
AromaUnitCallFile(...)
... |
Arguments passed to |
Methods:
extractCallArray |
- | |
extractCalls |
- | |
extractMatrix |
- | |
findUnitsTodo |
- | |
Methods inherited from AromaUnitSignalBinaryFile:
allocate, allocateFromUnitAnnotationDataFile, allocateFromUnitNamesFile, as.character, extractMatrix, extractRawGenomicSignals, fromFile, getChipType, getExtensionPattern, getFilenameExtension, getNumberOfFilesAveraged, getPlatform, isAverageFile, nbrOfUnits, readDataFrame, writeDataFrame
Methods inherited from AromaPlatformInterface:
getAromaPlatform, getAromaUflFile, getAromaUgpFile, getChipType, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith
Methods inherited from AromaTabularBinaryFile:
[, [<-, [[, allocate, as.character, colApply, colMeans, colStats, colSums, dimnames<-, getBytesPerColumn, getColClasses, getDefaultColumnNames, getRootName, importFrom, nbrOfColumns, nbrOfRows, readColumns, readDataFrame, readFooter, readHeader, readRawFooter, setAttributesByTags, subset, summary, updateData, updateDataColumn, writeFooter, writeRawFooter
Methods inherited from FileCacheKeyInterface:
getCacheKey
Methods inherited from CacheKeyInterface:
getCacheKey
Methods inherited from GenericTabularFile:
[, as.character, dim, extractMatrix, head, nbrOfColumns, nbrOfRows, readColumns, readDataFrame, tail, writeColumnsToFiles
Methods inherited from ColumnNamesInterface:
appendColumnNamesTranslator, appendColumnNamesTranslatorByNULL, appendColumnNamesTranslatorBycharacter, appendColumnNamesTranslatorByfunction, appendColumnNamesTranslatorBylist, clearColumnNamesTranslator, clearListOfColumnNamesTranslators, getColumnNames, getColumnNamesTranslator, getDefaultColumnNames, getListOfColumnNamesTranslators, nbrOfColumns, setColumnNames, setColumnNamesTranslator, setListOfColumnNamesTranslators, updateColumnNames
Methods inherited from GenericDataFile:
as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.core
Class AromaUnitCallSet
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFileSet
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
GenericTabularFileSet
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
AromaTabularBinarySet
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
AromaUnitSignalBinarySet
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaUnitCallSet
Directly known subclasses:
AromaUnitGenotypeCallSet
public static class AromaUnitCallSet
extends AromaUnitSignalBinarySet
An AromaUnitCallSet object represents a set of
AromaUnitCallFile
s with identical chip types.
AromaUnitCallSet(...)
AromaUnitCallSet(...)
... |
Arguments passed to |
Methods:
extractCallArray |
- | |
extractCalls |
- | |
extractGenotypeMatrix |
- | |
findUnitsTodo |
- | |
Methods inherited from AromaUnitSignalBinarySet:
byName, findByName, getAromaFullNameTranslatorSet, getAromaUgpFile, getChipType, getPlatform, validate, writeDataFrame
Methods inherited from AromaTabularBinarySet:
getDefaultFullName, getRootName, setAttributesBy, setAttributesBySampleAnnotationFile, setAttributesBySampleAnnotationSet, setAttributesByTags
Methods inherited from GenericTabularFileSet:
extractMatrix, calculateAverageColumnAcrossFiles
Methods inherited from GenericDataFileSet:
[, [[, anyDuplicated, anyNA, append, appendFiles, appendFullNamesTranslator, appendFullNamesTranslatorByNULL, appendFullNamesTranslatorByTabularTextFile, appendFullNamesTranslatorByTabularTextFileSet, appendFullNamesTranslatorBydata.frame, appendFullNamesTranslatorByfunction, appendFullNamesTranslatorBylist, as.character, as.list, byName, byPath, c, clearCache, clearFullNamesTranslator, clone, copyTo, dsApplyInPairs, duplicated, equals, extract, findByName, findDuplicated, getChecksum, getChecksumFileSet, getChecksumObjects, getDefaultFullName, getFile, getFileClass, getFileSize, getFiles, getFullNames, getNames, getOneFile, getPath, getPathnames, getSubdirs, gunzip, gzip, hasFile, indexOf, is.na, names, nbrOfFiles, rep, resetFullNames, setFullNamesTranslator, sortBy, unique, update2, updateFullName, updateFullNames, validate, getFullNameTranslatorSet, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.core
Class AromaUnitFracBCnBinaryFile
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
ColumnNamesInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
GenericTabularFile
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
CacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaTabularBinaryFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaUnitSignalBinaryFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaUnitFracBCnBinaryFile
Directly known subclasses:
public static class AromaUnitFracBCnBinaryFile
extends AromaUnitSignalBinaryFile
An AromaUnitFracBCnBinaryFile is a AromaUnitTabularBinaryFile
.
AromaUnitFracBCnBinaryFile(...)
AromaUnitFracBCnBinaryFile(...)
... |
Arguments passed to |
Methods:
extractRawAlleleBFractions |
- | |
Methods inherited from AromaUnitSignalBinaryFile:
allocate, allocateFromUnitAnnotationDataFile, allocateFromUnitNamesFile, as.character, extractMatrix, extractRawGenomicSignals, fromFile, getChipType, getExtensionPattern, getFilenameExtension, getNumberOfFilesAveraged, getPlatform, isAverageFile, nbrOfUnits, readDataFrame, writeDataFrame
Methods inherited from AromaPlatformInterface:
getAromaPlatform, getAromaUflFile, getAromaUgpFile, getChipType, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith
Methods inherited from AromaTabularBinaryFile:
[, [<-, [[, allocate, as.character, colApply, colMeans, colStats, colSums, dimnames<-, getBytesPerColumn, getColClasses, getDefaultColumnNames, getRootName, importFrom, nbrOfColumns, nbrOfRows, readColumns, readDataFrame, readFooter, readHeader, readRawFooter, setAttributesByTags, subset, summary, updateData, updateDataColumn, writeFooter, writeRawFooter
Methods inherited from FileCacheKeyInterface:
getCacheKey
Methods inherited from CacheKeyInterface:
getCacheKey
Methods inherited from GenericTabularFile:
[, as.character, dim, extractMatrix, head, nbrOfColumns, nbrOfRows, readColumns, readDataFrame, tail, writeColumnsToFiles
Methods inherited from ColumnNamesInterface:
appendColumnNamesTranslator, appendColumnNamesTranslatorByNULL, appendColumnNamesTranslatorBycharacter, appendColumnNamesTranslatorByfunction, appendColumnNamesTranslatorBylist, clearColumnNamesTranslator, clearListOfColumnNamesTranslators, getColumnNames, getColumnNamesTranslator, getDefaultColumnNames, getListOfColumnNamesTranslators, nbrOfColumns, setColumnNames, setColumnNamesTranslator, setListOfColumnNamesTranslators, updateColumnNames
Methods inherited from GenericDataFile:
as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.core
Class AromaUnitFracBCnBinarySet
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFileSet
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
GenericTabularFileSet
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
AromaTabularBinarySet
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
AromaUnitSignalBinarySet
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaUnitFracBCnBinarySet
Directly known subclasses:
public static class AromaUnitFracBCnBinarySet
extends AromaUnitSignalBinarySet
An AromaUnitFracBCnBinarySet object represents a set of
AromaUnitFracBCnBinaryFile
s with identical chip types.
AromaUnitFracBCnBinarySet(...)
AromaUnitFracBCnBinarySet(...)
... |
Arguments passed to |
The term "allele B fraction" is also know as "allele B frequency", which was coined by Peiffer et al. (2006). Note that the term "frequency" is a bit misleading since it is not a frequency in neither the statistical nor the population sense, but rather only proportion relative to the total amount of allele A and allele B signals, which is calculated for each sample independently.
Methods:
byName |
- | |
writeDataFrame |
- | |
Methods inherited from AromaUnitSignalBinarySet:
byName, findByName, getAromaFullNameTranslatorSet, getAromaUgpFile, getChipType, getPlatform, validate, writeDataFrame
Methods inherited from AromaTabularBinarySet:
getDefaultFullName, getRootName, setAttributesBy, setAttributesBySampleAnnotationFile, setAttributesBySampleAnnotationSet, setAttributesByTags
Methods inherited from GenericTabularFileSet:
extractMatrix, calculateAverageColumnAcrossFiles
Methods inherited from GenericDataFileSet:
[, [[, anyDuplicated, anyNA, append, appendFiles, appendFullNamesTranslator, appendFullNamesTranslatorByNULL, appendFullNamesTranslatorByTabularTextFile, appendFullNamesTranslatorByTabularTextFileSet, appendFullNamesTranslatorBydata.frame, appendFullNamesTranslatorByfunction, appendFullNamesTranslatorBylist, as.character, as.list, byName, byPath, c, clearCache, clearFullNamesTranslator, clone, copyTo, dsApplyInPairs, duplicated, equals, extract, findByName, findDuplicated, getChecksum, getChecksumFileSet, getChecksumObjects, getDefaultFullName, getFile, getFileClass, getFileSize, getFiles, getFullNames, getNames, getOneFile, getPath, getPathnames, getSubdirs, gunzip, gzip, hasFile, indexOf, is.na, names, nbrOfFiles, rep, resetFullNames, setFullNamesTranslator, sortBy, unique, update2, updateFullName, updateFullNames, validate, getFullNameTranslatorSet, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
[1] Peiffer et al., High-resolution genomic profiling of
chromosomal aberrations using Infinium whole-genome genotyping,
Genome Res, 2006.
Package: aroma.core
Class AromaUnitGenotypeCallFile
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
ColumnNamesInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
GenericTabularFile
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
CacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaTabularBinaryFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaUnitSignalBinaryFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaUnitCallFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaUnitGenotypeCallFile
Directly known subclasses:
public static class AromaUnitGenotypeCallFile
extends AromaUnitCallFile
An AromaUnitGenotypeCallFile is a AromaUnitTabularBinaryFile
.
AromaUnitGenotypeCallFile(...)
AromaUnitGenotypeCallFile(...)
... |
Arguments passed to |
Methods:
extractGenotypeMatrix |
- | |
extractGenotypes |
- | |
isHeterozygous |
- | |
isHomozygous |
- | |
updateGenotypes |
- | |
Methods inherited from AromaUnitCallFile:
allocate, extractCallArray, extractCalls, extractMatrix, findUnitsTodo
Methods inherited from AromaUnitSignalBinaryFile:
allocate, allocateFromUnitAnnotationDataFile, allocateFromUnitNamesFile, as.character, extractMatrix, extractRawGenomicSignals, fromFile, getChipType, getExtensionPattern, getFilenameExtension, getNumberOfFilesAveraged, getPlatform, isAverageFile, nbrOfUnits, readDataFrame, writeDataFrame
Methods inherited from AromaPlatformInterface:
getAromaPlatform, getAromaUflFile, getAromaUgpFile, getChipType, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith
Methods inherited from AromaTabularBinaryFile:
[, [<-, [[, allocate, as.character, colApply, colMeans, colStats, colSums, dimnames<-, getBytesPerColumn, getColClasses, getDefaultColumnNames, getRootName, importFrom, nbrOfColumns, nbrOfRows, readColumns, readDataFrame, readFooter, readHeader, readRawFooter, setAttributesByTags, subset, summary, updateData, updateDataColumn, writeFooter, writeRawFooter
Methods inherited from FileCacheKeyInterface:
getCacheKey
Methods inherited from CacheKeyInterface:
getCacheKey
Methods inherited from GenericTabularFile:
[, as.character, dim, extractMatrix, head, nbrOfColumns, nbrOfRows, readColumns, readDataFrame, tail, writeColumnsToFiles
Methods inherited from ColumnNamesInterface:
appendColumnNamesTranslator, appendColumnNamesTranslatorByNULL, appendColumnNamesTranslatorBycharacter, appendColumnNamesTranslatorByfunction, appendColumnNamesTranslatorBylist, clearColumnNamesTranslator, clearListOfColumnNamesTranslators, getColumnNames, getColumnNamesTranslator, getDefaultColumnNames, getListOfColumnNamesTranslators, nbrOfColumns, setColumnNames, setColumnNamesTranslator, setListOfColumnNamesTranslators, updateColumnNames
Methods inherited from GenericDataFile:
as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.core
Class AromaUnitGenotypeCallSet
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFileSet
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
GenericTabularFileSet
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
AromaTabularBinarySet
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
AromaUnitSignalBinarySet
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaUnitCallSet
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaUnitGenotypeCallSet
Directly known subclasses:
public static class AromaUnitGenotypeCallSet
extends AromaUnitCallSet
An AromaUnitGenotypeCallSet object represents a set of
AromaUnitGenotypeCallFile
s with identical chip types.
AromaUnitGenotypeCallSet(...)
AromaUnitGenotypeCallSet(...)
... |
Arguments passed to |
Methods:
byName |
- | |
extractGenotypes |
- | |
Methods inherited from AromaUnitCallSet:
byPath, extractCallArray, extractCalls, extractGenotypeMatrix, findByName, findUnitsTodo
Methods inherited from AromaUnitSignalBinarySet:
byName, findByName, getAromaFullNameTranslatorSet, getAromaUgpFile, getChipType, getPlatform, validate, writeDataFrame
Methods inherited from AromaTabularBinarySet:
getDefaultFullName, getRootName, setAttributesBy, setAttributesBySampleAnnotationFile, setAttributesBySampleAnnotationSet, setAttributesByTags
Methods inherited from GenericTabularFileSet:
extractMatrix, calculateAverageColumnAcrossFiles
Methods inherited from GenericDataFileSet:
[, [[, anyDuplicated, anyNA, append, appendFiles, appendFullNamesTranslator, appendFullNamesTranslatorByNULL, appendFullNamesTranslatorByTabularTextFile, appendFullNamesTranslatorByTabularTextFileSet, appendFullNamesTranslatorBydata.frame, appendFullNamesTranslatorByfunction, appendFullNamesTranslatorBylist, as.character, as.list, byName, byPath, c, clearCache, clearFullNamesTranslator, clone, copyTo, dsApplyInPairs, duplicated, equals, extract, findByName, findDuplicated, getChecksum, getChecksumFileSet, getChecksumObjects, getDefaultFullName, getFile, getFileClass, getFileSize, getFiles, getFullNames, getNames, getOneFile, getPath, getPathnames, getSubdirs, gunzip, gzip, hasFile, indexOf, is.na, names, nbrOfFiles, rep, resetFullNames, setFullNamesTranslator, sortBy, unique, update2, updateFullName, updateFullNames, validate, getFullNameTranslatorSet, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.core
Class AromaUnitPscnBinaryFile
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
ColumnNamesInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
GenericTabularFile
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
CacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaTabularBinaryFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaUnitSignalBinaryFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
CopyNumberDataFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaUnitPscnBinaryFile
Directly known subclasses:
public abstract static class AromaUnitPscnBinaryFile
extends CopyNumberDataFile
An AromaUnitPscnBinaryFile is a AromaUnitSignalBinaryFile
that holds total copy number signals (TCNs) and allele B fractions (BAFs).
The TCNs can either be on an unknown scale or ratios relative
to a reference. The signals are always stored on the original scale,
i.e. they are never stored on the logaritmic scale.
The BAFs are always on a [0-eps,1+eps] scale, where eps >= 0.
AromaUnitPscnBinaryFile(...)
AromaUnitPscnBinaryFile(...)
... |
Arguments passed to |
Methods:
extractRawCopyNumbers |
- | |
hasAlleleBFractions |
- | |
hasStrandiness |
- | |
hasTotalCopyNumberRatios |
- | |
Methods inherited from CopyNumberDataFile:
as, as.CopyNumberDataFile, getNumberOfFilesAveraged, hasAlleleBFractions, hasStrandiness
Methods inherited from AromaUnitSignalBinaryFile:
allocate, allocateFromUnitAnnotationDataFile, allocateFromUnitNamesFile, as.character, extractMatrix, extractRawGenomicSignals, fromFile, getChipType, getExtensionPattern, getFilenameExtension, getNumberOfFilesAveraged, getPlatform, isAverageFile, nbrOfUnits, readDataFrame, writeDataFrame
Methods inherited from AromaPlatformInterface:
getAromaPlatform, getAromaUflFile, getAromaUgpFile, getChipType, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith
Methods inherited from AromaTabularBinaryFile:
[, [<-, [[, allocate, as.character, colApply, colMeans, colStats, colSums, dimnames<-, getBytesPerColumn, getColClasses, getDefaultColumnNames, getRootName, importFrom, nbrOfColumns, nbrOfRows, readColumns, readDataFrame, readFooter, readHeader, readRawFooter, setAttributesByTags, subset, summary, updateData, updateDataColumn, writeFooter, writeRawFooter
Methods inherited from FileCacheKeyInterface:
getCacheKey
Methods inherited from CacheKeyInterface:
getCacheKey
Methods inherited from GenericTabularFile:
[, as.character, dim, extractMatrix, head, nbrOfColumns, nbrOfRows, readColumns, readDataFrame, tail, writeColumnsToFiles
Methods inherited from ColumnNamesInterface:
appendColumnNamesTranslator, appendColumnNamesTranslatorByNULL, appendColumnNamesTranslatorBycharacter, appendColumnNamesTranslatorByfunction, appendColumnNamesTranslatorBylist, clearColumnNamesTranslator, clearListOfColumnNamesTranslators, getColumnNames, getColumnNamesTranslator, getDefaultColumnNames, getListOfColumnNamesTranslators, nbrOfColumns, setColumnNames, setColumnNamesTranslator, setListOfColumnNamesTranslators, updateColumnNames
Methods inherited from GenericDataFile:
as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.core
Class AromaUnitPscnBinarySet
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFileSet
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
GenericTabularFileSet
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
AromaTabularBinarySet
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
AromaUnitSignalBinarySet
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
CopyNumberDataSet
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaUnitPscnBinarySet
Directly known subclasses:
public static class AromaUnitPscnBinarySet
extends CopyNumberDataSet
An AromaUnitPscnBinarySet object represents a set of
AromaUnitPscnBinaryFile
s with identical chip types.
AromaUnitPscnBinarySet(...)
AromaUnitPscnBinarySet(...)
... |
Arguments passed to |
Methods:
byName |
- | |
getAverageFile |
- | |
writeDataFrame |
- | |
Methods inherited from CopyNumberDataSet:
as, as.CopyNumberDataSet, doCBS, hasAlleleBFractions, hasStrandiness
Methods inherited from AromaUnitSignalBinarySet:
byName, findByName, getAromaFullNameTranslatorSet, getAromaUgpFile, getChipType, getPlatform, validate, writeDataFrame
Methods inherited from AromaTabularBinarySet:
getDefaultFullName, getRootName, setAttributesBy, setAttributesBySampleAnnotationFile, setAttributesBySampleAnnotationSet, setAttributesByTags
Methods inherited from GenericTabularFileSet:
extractMatrix, calculateAverageColumnAcrossFiles
Methods inherited from GenericDataFileSet:
[, [[, anyDuplicated, anyNA, append, appendFiles, appendFullNamesTranslator, appendFullNamesTranslatorByNULL, appendFullNamesTranslatorByTabularTextFile, appendFullNamesTranslatorByTabularTextFileSet, appendFullNamesTranslatorBydata.frame, appendFullNamesTranslatorByfunction, appendFullNamesTranslatorBylist, as.character, as.list, byName, byPath, c, clearCache, clearFullNamesTranslator, clone, copyTo, dsApplyInPairs, duplicated, equals, extract, findByName, findDuplicated, getChecksum, getChecksumFileSet, getChecksumObjects, getDefaultFullName, getFile, getFileClass, getFileSize, getFiles, getFullNames, getNames, getOneFile, getPath, getPathnames, getSubdirs, gunzip, gzip, hasFile, indexOf, is.na, names, nbrOfFiles, rep, resetFullNames, setFullNamesTranslator, sortBy, unique, update2, updateFullName, updateFullNames, validate, getFullNameTranslatorSet, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.core
Class AromaUnitSignalBinaryFile
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
ColumnNamesInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
GenericTabularFile
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
CacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaTabularBinaryFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaUnitSignalBinaryFile
Directly known subclasses:
AromaUnitCallFile, AromaUnitFracBCnBinaryFile, AromaUnitGenotypeCallFile, AromaUnitPscnBinaryFile, AromaUnitTotalCnBinaryFile, AromaUnitTypesFile
public static class AromaUnitSignalBinaryFile
extends AromaPlatformInterface
An AromaUnitSignalBinaryFile is a AromaTabularBinaryFile
.
AromaUnitSignalBinaryFile(...)
AromaUnitSignalBinaryFile(...)
... |
Arguments passed to |
Methods:
extractMatrix |
- | |
getChipType |
- | |
getNumberOfFilesAveraged |
- | |
getPlatform |
- | |
isAverageFile |
- | |
nbrOfUnits |
- | |
readDataFrame |
- | |
writeDataFrame |
Writes the data file as a tab-delimited text file. | |
Methods inherited from AromaPlatformInterface:
getAromaPlatform, getAromaUflFile, getAromaUgpFile, getChipType, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith
Methods inherited from AromaTabularBinaryFile:
[, [<-, [[, allocate, as.character, colApply, colMeans, colStats, colSums, dimnames<-, getBytesPerColumn, getColClasses, getDefaultColumnNames, getRootName, importFrom, nbrOfColumns, nbrOfRows, readColumns, readDataFrame, readFooter, readHeader, readRawFooter, setAttributesByTags, subset, summary, updateData, updateDataColumn, writeFooter, writeRawFooter
Methods inherited from FileCacheKeyInterface:
getCacheKey
Methods inherited from CacheKeyInterface:
getCacheKey
Methods inherited from GenericTabularFile:
[, as.character, dim, extractMatrix, head, nbrOfColumns, nbrOfRows, readColumns, readDataFrame, tail, writeColumnsToFiles
Methods inherited from ColumnNamesInterface:
appendColumnNamesTranslator, appendColumnNamesTranslatorByNULL, appendColumnNamesTranslatorBycharacter, appendColumnNamesTranslatorByfunction, appendColumnNamesTranslatorBylist, clearColumnNamesTranslator, clearListOfColumnNamesTranslators, getColumnNames, getColumnNamesTranslator, getDefaultColumnNames, getListOfColumnNamesTranslators, nbrOfColumns, setColumnNames, setColumnNamesTranslator, setListOfColumnNamesTranslators, updateColumnNames
Methods inherited from GenericDataFile:
as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.core
Class AromaUnitSignalBinarySet
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFileSet
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
GenericTabularFileSet
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
AromaTabularBinarySet
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
AromaUnitSignalBinarySet
Directly known subclasses:
AromaUnitCallSet, AromaUnitFracBCnBinarySet, AromaUnitGenotypeCallSet, AromaUnitPscnBinarySet, AromaUnitTotalCnBinarySet
public static class AromaUnitSignalBinarySet
extends AromaTabularBinarySet
An AromaUnitSignalBinarySet object represents a set of
AromaUnitSignalBinaryFile
s with identical chip types.
AromaUnitSignalBinarySet(...)
AromaUnitSignalBinarySet(...)
... |
Arguments passed to |
Methods:
byName |
- | |
getAromaUgpFile |
- | |
getChipType |
- | |
getPlatform |
- | |
writeDataFrame |
Writes the data set as a tab-delimited text file. | |
Methods inherited from AromaTabularBinarySet:
getDefaultFullName, getRootName, setAttributesBy, setAttributesBySampleAnnotationFile, setAttributesBySampleAnnotationSet, setAttributesByTags
Methods inherited from GenericTabularFileSet:
extractMatrix, calculateAverageColumnAcrossFiles
Methods inherited from GenericDataFileSet:
[, [[, anyDuplicated, anyNA, append, appendFiles, appendFullNamesTranslator, appendFullNamesTranslatorByNULL, appendFullNamesTranslatorByTabularTextFile, appendFullNamesTranslatorByTabularTextFileSet, appendFullNamesTranslatorBydata.frame, appendFullNamesTranslatorByfunction, appendFullNamesTranslatorBylist, as.character, as.list, byName, byPath, c, clearCache, clearFullNamesTranslator, clone, copyTo, dsApplyInPairs, duplicated, equals, extract, findByName, findDuplicated, getChecksum, getChecksumFileSet, getChecksumObjects, getDefaultFullName, getFile, getFileClass, getFileSize, getFiles, getFullNames, getNames, getOneFile, getPath, getPathnames, getSubdirs, gunzip, gzip, hasFile, indexOf, is.na, names, nbrOfFiles, rep, resetFullNames, setFullNamesTranslator, sortBy, unique, update2, updateFullName, updateFullNames, validate, getFullNameTranslatorSet, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.core
Class AromaUnitTabularBinaryFile
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
ColumnNamesInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
GenericTabularFile
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
CacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaTabularBinaryFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaMicroarrayTabularBinaryFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
UnitAnnotationDataFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaUnitTabularBinaryFile
Directly known subclasses:
AromaUflFile, AromaUgcFile, AromaUgpFile, AromaUnitChromosomeTabularBinaryFile, AromaUnitGcContentFile
public abstract static class AromaUnitTabularBinaryFile
extends UnitAnnotationDataFile
A AromaUnitTabularBinaryFile is an AromaTabularBinaryFile
with
the constraint that the rows map one-to-one to, and in the same order as,
the units in a annotation chip type file (e.g. CDF file).
The (full) chip type of the annotation chip type file is given by the
mandatory file footer chipType
.
AromaUnitTabularBinaryFile(...)
AromaUnitTabularBinaryFile(...)
... |
Arguments passed to |
Methods:
byChipType |
- | |
nbrOfUnits |
- | |
writeDataFrame |
Writes the data file as a tab-delimited text file. | |
Methods inherited from UnitAnnotationDataFile:
byChipType, getAromaUflFile, getAromaUgpFile, getChipType, getDefaultExtension, getPlatform, nbrOfUnits
Methods inherited from AromaMicroarrayTabularBinaryFile:
allocate, as.character, byChipType, findByChipType, getChipType, getFilenameExtension, getPlatform
Methods inherited from AromaPlatformInterface:
getAromaPlatform, getAromaUflFile, getAromaUgpFile, getChipType, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith
Methods inherited from AromaTabularBinaryFile:
[, [<-, [[, allocate, as.character, colApply, colMeans, colStats, colSums, dimnames<-, getBytesPerColumn, getColClasses, getDefaultColumnNames, getRootName, importFrom, nbrOfColumns, nbrOfRows, readColumns, readDataFrame, readFooter, readHeader, readRawFooter, setAttributesByTags, subset, summary, updateData, updateDataColumn, writeFooter, writeRawFooter
Methods inherited from FileCacheKeyInterface:
getCacheKey
Methods inherited from CacheKeyInterface:
getCacheKey
Methods inherited from GenericTabularFile:
[, as.character, dim, extractMatrix, head, nbrOfColumns, nbrOfRows, readColumns, readDataFrame, tail, writeColumnsToFiles
Methods inherited from ColumnNamesInterface:
appendColumnNamesTranslator, appendColumnNamesTranslatorByNULL, appendColumnNamesTranslatorBycharacter, appendColumnNamesTranslatorByfunction, appendColumnNamesTranslatorBylist, clearColumnNamesTranslator, clearListOfColumnNamesTranslators, getColumnNames, getColumnNamesTranslator, getDefaultColumnNames, getListOfColumnNamesTranslators, nbrOfColumns, setColumnNames, setColumnNamesTranslator, setListOfColumnNamesTranslators, updateColumnNames
Methods inherited from GenericDataFile:
as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.core
Class AromaUnitTotalCnBinaryFile
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
ColumnNamesInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
GenericTabularFile
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
CacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaTabularBinaryFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaUnitSignalBinaryFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
CopyNumberDataFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaUnitTotalCnBinaryFile
Directly known subclasses:
public abstract static class AromaUnitTotalCnBinaryFile
extends CopyNumberDataFile
An AromaUnitTotalCnBinaryFile is a AromaUnitSignalBinaryFile
.
AromaUnitTotalCnBinaryFile(...)
AromaUnitTotalCnBinaryFile(...)
... |
Arguments passed to |
Methods:
extractPSCNArray |
- | |
extractPSCNMatrix |
- | |
extractRawCopyNumbers |
- | |
getAM |
- | |
hasAlleleBFractions |
- | |
hasStrandiness |
- | |
Methods inherited from CopyNumberDataFile:
as, as.CopyNumberDataFile, getNumberOfFilesAveraged, hasAlleleBFractions, hasStrandiness
Methods inherited from AromaUnitSignalBinaryFile:
allocate, allocateFromUnitAnnotationDataFile, allocateFromUnitNamesFile, as.character, extractMatrix, extractRawGenomicSignals, fromFile, getChipType, getExtensionPattern, getFilenameExtension, getNumberOfFilesAveraged, getPlatform, isAverageFile, nbrOfUnits, readDataFrame, writeDataFrame
Methods inherited from AromaPlatformInterface:
getAromaPlatform, getAromaUflFile, getAromaUgpFile, getChipType, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith
Methods inherited from AromaTabularBinaryFile:
[, [<-, [[, allocate, as.character, colApply, colMeans, colStats, colSums, dimnames<-, getBytesPerColumn, getColClasses, getDefaultColumnNames, getRootName, importFrom, nbrOfColumns, nbrOfRows, readColumns, readDataFrame, readFooter, readHeader, readRawFooter, setAttributesByTags, subset, summary, updateData, updateDataColumn, writeFooter, writeRawFooter
Methods inherited from FileCacheKeyInterface:
getCacheKey
Methods inherited from CacheKeyInterface:
getCacheKey
Methods inherited from GenericTabularFile:
[, as.character, dim, extractMatrix, head, nbrOfColumns, nbrOfRows, readColumns, readDataFrame, tail, writeColumnsToFiles
Methods inherited from ColumnNamesInterface:
appendColumnNamesTranslator, appendColumnNamesTranslatorByNULL, appendColumnNamesTranslatorBycharacter, appendColumnNamesTranslatorByfunction, appendColumnNamesTranslatorBylist, clearColumnNamesTranslator, clearListOfColumnNamesTranslators, getColumnNames, getColumnNamesTranslator, getDefaultColumnNames, getListOfColumnNamesTranslators, nbrOfColumns, setColumnNames, setColumnNamesTranslator, setListOfColumnNamesTranslators, updateColumnNames
Methods inherited from GenericDataFile:
as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.core
Class AromaUnitTotalCnBinarySet
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFileSet
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
GenericTabularFileSet
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
AromaTabularBinarySet
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
AromaUnitSignalBinarySet
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
CopyNumberDataSet
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaUnitTotalCnBinarySet
Directly known subclasses:
public static class AromaUnitTotalCnBinarySet
extends CopyNumberDataSet
An AromaUnitTotalCnBinarySet object represents a set of
AromaUnitTotalCnBinaryFile
s with identical chip types.
AromaUnitTotalCnBinarySet(...)
AromaUnitTotalCnBinarySet(...)
... |
Arguments passed to |
Methods:
as.AromaUnitTotalCnBinarySetTuple |
- | |
as.CopyNumberDataSetTuple |
- | |
byName |
- | |
exportAromaUnitPscnBinarySet |
- | |
exportTotalCnRatioSet |
- | |
extractPSCNArray |
- | |
getAverageFile |
- | |
getUnitNamesFile |
- | |
writeDataFrame |
- | |
Methods inherited from CopyNumberDataSet:
as, as.CopyNumberDataSet, doCBS, hasAlleleBFractions, hasStrandiness
Methods inherited from AromaUnitSignalBinarySet:
byName, findByName, getAromaFullNameTranslatorSet, getAromaUgpFile, getChipType, getPlatform, validate, writeDataFrame
Methods inherited from AromaTabularBinarySet:
getDefaultFullName, getRootName, setAttributesBy, setAttributesBySampleAnnotationFile, setAttributesBySampleAnnotationSet, setAttributesByTags
Methods inherited from GenericTabularFileSet:
extractMatrix, calculateAverageColumnAcrossFiles
Methods inherited from GenericDataFileSet:
[, [[, anyDuplicated, anyNA, append, appendFiles, appendFullNamesTranslator, appendFullNamesTranslatorByNULL, appendFullNamesTranslatorByTabularTextFile, appendFullNamesTranslatorByTabularTextFileSet, appendFullNamesTranslatorBydata.frame, appendFullNamesTranslatorByfunction, appendFullNamesTranslatorBylist, as.character, as.list, byName, byPath, c, clearCache, clearFullNamesTranslator, clone, copyTo, dsApplyInPairs, duplicated, equals, extract, findByName, findDuplicated, getChecksum, getChecksumFileSet, getChecksumObjects, getDefaultFullName, getFile, getFileClass, getFileSize, getFiles, getFullNames, getNames, getOneFile, getPath, getPathnames, getSubdirs, gunzip, gzip, hasFile, indexOf, is.na, names, nbrOfFiles, rep, resetFullNames, setFullNamesTranslator, sortBy, unique, update2, updateFullName, updateFullNames, validate, getFullNameTranslatorSet, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.core
Class AromaUnitTypesFile
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
ColumnNamesInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
GenericTabularFile
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
CacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
FileCacheKeyInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaTabularBinaryFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaUnitSignalBinaryFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
UnitAnnotationDataFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
UnitTypesFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
AromaUnitTypesFile
Directly known subclasses:
public static class AromaUnitTypesFile
extends UnitTypesFile
AromaUnitTypesFile(...)
AromaUnitTypesFile(...)
... |
Arguments passed to |
Methods:
getChipType |
- | |
getPlatform |
- | |
getUnitTypes |
- | |
importFromUnitTypesFile |
- | |
Methods inherited from UnitTypesFile:
getUnitTypes, nbrOfUnits
Methods inherited from UnitAnnotationDataFile:
byChipType, getAromaUflFile, getAromaUgpFile, getChipType, getDefaultExtension, getPlatform, nbrOfUnits
Methods inherited from AromaUnitSignalBinaryFile:
allocate, allocateFromUnitAnnotationDataFile, allocateFromUnitNamesFile, as.character, extractMatrix, extractRawGenomicSignals, fromFile, getChipType, getExtensionPattern, getFilenameExtension, getNumberOfFilesAveraged, getPlatform, isAverageFile, nbrOfUnits, readDataFrame, writeDataFrame
Methods inherited from AromaPlatformInterface:
getAromaPlatform, getAromaUflFile, getAromaUgpFile, getChipType, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith
Methods inherited from AromaTabularBinaryFile:
[, [<-, [[, allocate, as.character, colApply, colMeans, colStats, colSums, dimnames<-, getBytesPerColumn, getColClasses, getDefaultColumnNames, getRootName, importFrom, nbrOfColumns, nbrOfRows, readColumns, readDataFrame, readFooter, readHeader, readRawFooter, setAttributesByTags, subset, summary, updateData, updateDataColumn, writeFooter, writeRawFooter
Methods inherited from FileCacheKeyInterface:
getCacheKey
Methods inherited from CacheKeyInterface:
getCacheKey
Methods inherited from GenericTabularFile:
[, as.character, dim, extractMatrix, head, nbrOfColumns, nbrOfRows, readColumns, readDataFrame, tail, writeColumnsToFiles
Methods inherited from ColumnNamesInterface:
appendColumnNamesTranslator, appendColumnNamesTranslatorByNULL, appendColumnNamesTranslatorBycharacter, appendColumnNamesTranslatorByfunction, appendColumnNamesTranslatorBylist, clearColumnNamesTranslator, clearListOfColumnNamesTranslators, getColumnNames, getColumnNamesTranslator, getDefaultColumnNames, getListOfColumnNamesTranslators, nbrOfColumns, setColumnNames, setColumnNamesTranslator, setListOfColumnNamesTranslators, updateColumnNames
Methods inherited from GenericDataFile:
as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum, getParentName
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.core
Class BinnedScatter
list
~~|
~~+--
BinnedScatter
Directly known subclasses:
public class BinnedScatter
extends list
BinnedScatter(data=NULL, density=NULL, map=NULL, params=NULL)
BinnedScatter(data=NULL, density=NULL, map=NULL, params=NULL)
data |
|
density |
... |
map |
... |
params |
A |
Methods:
plot |
- | |
points |
- | |
reorder |
- | |
subsample |
- | |
subset |
- | |
Methods inherited from list:
Ops,nonStructure,vector-method, Ops,structure,vector-method, Ops,vector,nonStructure-method, Ops,vector,structure-method, all.equal, as.CopyNumberDataSetTuple, as.data.frame, attachLocally, callHooks, coerce,ANY,list-method, exportAromaUnitPscnBinarySet, listToXml, mergeBoxplotStats, relist, type.convert, within
Henrik Bengtsson
The spatial density is estimated by internal functions of the smoothScatter package.
# Sample scatter data n <- 10e3 x <- rnorm(n=n) y <- rnorm(n=n) xy <- cbind(x=x, y=sin(x)+y/5) # Bin data and estimate densities xyd <- binScatter(xy) layout(matrix(1:4, nrow=2)) par(mar=c(5,4,2,1)) # Plot data plot(xyd, pch=1) # Thin scatter data by subsampling rhos <- c(1/3, 1/4, 1/6) for (kk in seq_along(rhos)) { xyd2 <- subsample(xyd, size=rhos[kk]) points(xyd2, pch=1, col=kk+1) } for (kk in seq_along(rhos)) { xyd2 <- subsample(xyd, size=rhos[kk]) plot(xyd2, pch=1, col=kk+1) mtext(side=3, line=0, sprintf("Density: %.1f%%", 100*rhos[kk])) }
# Sample scatter data n <- 10e3 x <- rnorm(n=n) y <- rnorm(n=n) xy <- cbind(x=x, y=sin(x)+y/5) # Bin data and estimate densities xyd <- binScatter(xy) layout(matrix(1:4, nrow=2)) par(mar=c(5,4,2,1)) # Plot data plot(xyd, pch=1) # Thin scatter data by subsampling rhos <- c(1/3, 1/4, 1/6) for (kk in seq_along(rhos)) { xyd2 <- subsample(xyd, size=rhos[kk]) points(xyd2, pch=1, col=kk+1) } for (kk in seq_along(rhos)) { xyd2 <- subsample(xyd, size=rhos[kk]) plot(xyd2, pch=1, col=kk+1) mtext(side=3, line=0, sprintf("Density: %.1f%%", 100*rhos[kk])) }
Package: aroma.core
Class CbsModel
Object
~~|
~~+--
ChromosomalModel
~~~~~~~|
~~~~~~~+--
CopyNumberChromosomalModel
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
CopyNumberSegmentationModel
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
CbsModel
Directly known subclasses:
public static class CbsModel
extends CopyNumberSegmentationModel
This class represents the Circular Binary Segmentation (CBS) model [1].
CbsModel(cesTuple=NULL, ..., seed=NULL)
CbsModel(cesTuple=NULL, ..., seed=NULL)
cesTuple |
|
... |
Arguments passed to the constructor of
|
seed |
An (optional) |
Methods:
No methods defined.
Methods inherited from CopyNumberSegmentationModel:
fit, getAsteriskTags, getFitFunction, getFullNames, getRegions, getTags, plot, plotCopyNumberRegionLayers, writeRegions
Methods inherited from CopyNumberChromosomalModel:
as.character, calculateChromosomeStatistics, calculateRatios, estimateSds, extractRawCopyNumbers, fit, getChromosomeLength, getDataFileMatrix, getMaxNAFraction, getNames, getOptionalArguments, getPairedNames, getRefSetTuple, getReference, getReferenceSetTuple, isPaired, newPlot, plotAxesLayers, plotChromosomesLayers, plotCytobandLayers, plotFitLayers, plotGridHorizontalLayers, plotRawCopyNumbers, plotSampleLayers, setReference
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
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
[1] Olshen, A. B., Venkatraman, E. S., Lucito, R., Wigler, M.
Circular binary segmentation for the analysis of array-based
DNA copy number data. Biostatistics 5: 557-572, 2004.
[2] Venkatraman, E. S. & Olshen, A. B.
A faster circular binary segmentation algorithm for the
analysis of array CGH data. Bioinformatics, 2007.
Package: aroma.core
Class ChromosomalModel
Object
~~|
~~+--
ChromosomalModel
Directly known subclasses:
CbsModel, CopyNumberChromosomalModel, CopyNumberSegmentationModel, GladModel, HaarSegModel, RawCopyNumberModel
public abstract static class ChromosomalModel
extends Object
This abstract class represents a chromosomal model.
ChromosomalModel(cesTuple=NULL, tags="*", genome="Human", chromosomes=NULL, ...)
ChromosomalModel(cesTuple=NULL, tags="*", genome="Human", chromosomes=NULL, ...)
cesTuple |
|
tags |
|
genome |
A |
chromosomes |
(optional) A |
... |
Not used. |
Methods:
fit |
- | |
getChipType |
Gets a label for all chip types merged. | |
getChipTypes |
- | |
getChromosomes |
Gets the chromosomes to be processed. | |
getFullName |
- | |
getFullNames |
- | |
getGenome |
- | |
getName |
- | |
getNames |
Gets the names of the arrays. | |
getPath |
- | |
getSets |
- | |
getTags |
- | |
indexOf |
- | |
nbrOfArrays |
Gets the number of arrays. | |
nbrOfChipTypes |
Gets the number of chip types. | |
setChromosomes |
- | |
setGenome |
- | |
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
This class requires genome information annotation files for every chip type.
Henrik Bengtsson
Package: aroma.core
Class ChromosomeExplorer
Object
~~|
~~+--
Explorer
~~~~~~~|
~~~~~~~+--
ChromosomeExplorer
Directly known subclasses:
public static class ChromosomeExplorer
extends Explorer
ChromosomeExplorer(model=NULL, zooms=2^(0:6), ...)
ChromosomeExplorer(model=NULL, zooms=2^(0:6), ...)
model |
A |
zooms |
An positive |
... |
Not used. |
Methods:
display |
- | |
getChromosomes |
Gets the chromosomes available. | |
getFullNames |
- | |
getModel |
Gets the model. | |
getNames |
- | |
getPath |
- | |
getZooms |
- | |
indexOf |
- | |
process |
Generates image files, scripts and dynamic pages for the explorer. | |
setArrays |
Sets the arrays. | |
setCytoband |
- | |
setZooms |
- | |
Methods inherited from Explorer:
addIncludes, addIndexFile, as.character, display, getAlias, getArraysOfInput, getAsteriskTags, getFullName, getIncludePath, getMainPath, getName, getNameOfInput, getNames, getPath, getReportPathPattern, getRootPath, getSampleLayerPrefix, getSubname, getTags, getTagsOfInput, getTemplatePath, getVersion, nbrOfArrays, process, setAlias, setArrays, setReportPathPattern, setSubname, setup, splitByReportPathPattern, updateSetupExplorerFile
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
In order to get better looking graphs, but also to be able to generate
bitmap images on systems without direct bitmap support, which is the case
when running R in batch mode or on Unix without X11 support, images are
created using the png2
device (a wrapper for
bitmap()
imitating png()
). The png()
is only
used if png2()
, which requires Ghostscript, does not.
Note, when images are created using png2()
, the images does
not appear immediately, although the function call is completed,
so be patient.
Henrik Bengtsson
Binned smoothing of a matrix column by column.
## S3 method for class 'matrix' colBinnedSmoothing(Y, x=seq_len(nrow(Y)), w=NULL, xOut=NULL, xOutRange=NULL, from=min(x, na.rm = TRUE), to=max(x, na.rm = TRUE), by=NULL, length.out=length(x), na.rm=TRUE, FUN="median", ..., verbose=FALSE)
## S3 method for class 'matrix' colBinnedSmoothing(Y, x=seq_len(nrow(Y)), w=NULL, xOut=NULL, xOutRange=NULL, from=min(x, na.rm = TRUE), to=max(x, na.rm = TRUE), by=NULL, length.out=length(x), na.rm=TRUE, FUN="median", ..., verbose=FALSE)
Y |
|
x |
A (optional) |
w |
A optional |
xOut |
|
xOutRange |
Optional Kx2 |
from , to , by , length.out
|
If neither |
FUN |
A |
na.rm |
If |
... |
Not used. |
verbose |
See |
Note that all zero-length bins will get result
in an
NA
value, because such bins contain no data points.
This also means that colBinnedSmoothing(Y, x=x, xOut=xOut)
where xOut
contains duplicated values, will result in
some zero-length bins and hence NA
values.
Returns a numeric
KxI matrix
(or a vector
of length K) where
K is the total number of bins.
The following attributes are also returned:
xOut
The center locations of each bin.
xOutRange
The bin boundaries.
count
The number of data points within each bin
(based solely on argument x
).
binWidth
The average bin width.
Henrik Bengtsson
# Number of tracks I <- 4 # Number of data points per track J <- 100 # Simulate data with a gain in track 2 and 3 x <- 1:J Y <- matrix(rnorm(I*J, sd=1/2), ncol=I) Y[30:50,2:3] <- Y[30:50,2:3] + 3 # Uniformly distributed equal-sized bins Ys3 <- colBinnedSmoothing(Y, x=x, from=2, by=3) Ys5 <- colBinnedSmoothing(Y, x=x, from=3, by=5) # Custom bins xOutRange <- t(matrix(c( 1, 11, 11, 31, 31, 41, 41, 51, 51, 81, 81, 91, 91,101 ), nrow=2)) YsC <- colBinnedSmoothing(Y, x=x, xOutRange=xOutRange) # Custom bins specified by center locations with # maximized width relative to the neighboring bins. xOut <- c(6, 21, 36, 46, 66, 86, 96) YsD <- colBinnedSmoothing(Y, x=x, xOut=xOut) xlim <- range(x) ylim <- c(-3,5) layout(matrix(1:I, ncol=1)) par(mar=c(3,3,1,1)+0.1, pch=19) for (ii in 1:I) { plot(NA, xlim=xlim, ylim=ylim) points(x, Y[,ii], col="#999999") xOut <- attr(Ys3, "xOut") lines(xOut, Ys3[,ii], col=2) points(xOut, Ys3[,ii], col=2) xOut <- attr(Ys5, "xOut") lines(xOut, Ys5[,ii], col=3) points(xOut, Ys5[,ii], col=3) xOut <- attr(YsC, "xOut") lines(xOut, YsC[,ii], col=4) points(xOut, YsC[,ii], col=4, pch=15) xOut <- attr(YsD, "xOut") lines(xOut, YsD[,ii], col=5) points(xOut, YsD[,ii], col=5, pch=15) if (ii == 1) { legend("topright", pch=c(19,19,15,15), col=c(2,3,4,5), c("by=3", "by=5", "Custom #1", "Custom #2"), horiz=TRUE, bty="n") } } # Sanity checks xOut <- x YsT <- colBinnedSmoothing(Y, x=x, xOut=xOut) stopifnot(all(YsT == Y)) stopifnot(all(attr(YsT, "counts") == 1)) xOut <- attr(YsD, "xOut") YsE <- colBinnedSmoothing(YsD, x=xOut, xOut=xOut) stopifnot(all(YsE == YsD)) stopifnot(all(attr(YsE, "xOutRange") == attr(YsD, "xOutRange"))) stopifnot(all(attr(YsE, "counts") == 1)) # Scramble ordering of loci idxs <- sample(x) x2 <- x[idxs] Y2 <- Y[idxs,,drop=FALSE] Y2s <- colBinnedSmoothing(Y2, x=x2, xOut=x2) stopifnot(all(attr(Y2s, "xOut") == x2)) stopifnot(all(attr(Y2s, "counts") == 1)) stopifnot(all(Y2s == Y2)) xOut <- x[seq(from=2, to=J, by=3)] YsT <- colBinnedSmoothing(Y, x=x, xOut=xOut) stopifnot(all(YsT == Ys3)) stopifnot(all(attr(YsT, "counts") == 3)) xOut <- x[seq(from=3, to=J, by=5)] YsT <- colBinnedSmoothing(Y, x=x, xOut=xOut) stopifnot(all(YsT == Ys5)) stopifnot(all(attr(YsT, "counts") == 5))
# Number of tracks I <- 4 # Number of data points per track J <- 100 # Simulate data with a gain in track 2 and 3 x <- 1:J Y <- matrix(rnorm(I*J, sd=1/2), ncol=I) Y[30:50,2:3] <- Y[30:50,2:3] + 3 # Uniformly distributed equal-sized bins Ys3 <- colBinnedSmoothing(Y, x=x, from=2, by=3) Ys5 <- colBinnedSmoothing(Y, x=x, from=3, by=5) # Custom bins xOutRange <- t(matrix(c( 1, 11, 11, 31, 31, 41, 41, 51, 51, 81, 81, 91, 91,101 ), nrow=2)) YsC <- colBinnedSmoothing(Y, x=x, xOutRange=xOutRange) # Custom bins specified by center locations with # maximized width relative to the neighboring bins. xOut <- c(6, 21, 36, 46, 66, 86, 96) YsD <- colBinnedSmoothing(Y, x=x, xOut=xOut) xlim <- range(x) ylim <- c(-3,5) layout(matrix(1:I, ncol=1)) par(mar=c(3,3,1,1)+0.1, pch=19) for (ii in 1:I) { plot(NA, xlim=xlim, ylim=ylim) points(x, Y[,ii], col="#999999") xOut <- attr(Ys3, "xOut") lines(xOut, Ys3[,ii], col=2) points(xOut, Ys3[,ii], col=2) xOut <- attr(Ys5, "xOut") lines(xOut, Ys5[,ii], col=3) points(xOut, Ys5[,ii], col=3) xOut <- attr(YsC, "xOut") lines(xOut, YsC[,ii], col=4) points(xOut, YsC[,ii], col=4, pch=15) xOut <- attr(YsD, "xOut") lines(xOut, YsD[,ii], col=5) points(xOut, YsD[,ii], col=5, pch=15) if (ii == 1) { legend("topright", pch=c(19,19,15,15), col=c(2,3,4,5), c("by=3", "by=5", "Custom #1", "Custom #2"), horiz=TRUE, bty="n") } } # Sanity checks xOut <- x YsT <- colBinnedSmoothing(Y, x=x, xOut=xOut) stopifnot(all(YsT == Y)) stopifnot(all(attr(YsT, "counts") == 1)) xOut <- attr(YsD, "xOut") YsE <- colBinnedSmoothing(YsD, x=xOut, xOut=xOut) stopifnot(all(YsE == YsD)) stopifnot(all(attr(YsE, "xOutRange") == attr(YsD, "xOutRange"))) stopifnot(all(attr(YsE, "counts") == 1)) # Scramble ordering of loci idxs <- sample(x) x2 <- x[idxs] Y2 <- Y[idxs,,drop=FALSE] Y2s <- colBinnedSmoothing(Y2, x=x2, xOut=x2) stopifnot(all(attr(Y2s, "xOut") == x2)) stopifnot(all(attr(Y2s, "counts") == 1)) stopifnot(all(Y2s == Y2)) xOut <- x[seq(from=2, to=J, by=3)] YsT <- colBinnedSmoothing(Y, x=x, xOut=xOut) stopifnot(all(YsT == Ys3)) stopifnot(all(attr(YsT, "counts") == 3)) xOut <- x[seq(from=3, to=J, by=5)] YsT <- colBinnedSmoothing(Y, x=x, xOut=xOut) stopifnot(all(YsT == Ys5)) stopifnot(all(attr(YsT, "counts") == 5))
Kernel smoothing of a matrix column by column.
## S3 method for class 'matrix' colKernelSmoothing(Y, x=seq_len(nrow(Y)), w=NULL, xOut=x, kernel=c("gaussian", "uniform"), h, censorH=3, na.rm=TRUE, robust=FALSE, ..., verbose=FALSE)
## S3 method for class 'matrix' colKernelSmoothing(Y, x=seq_len(nrow(Y)), w=NULL, xOut=x, kernel=c("gaussian", "uniform"), h, censorH=3, na.rm=TRUE, robust=FALSE, ..., verbose=FALSE)
Y |
|
x |
A (optional) |
w |
A optional |
xOut |
A |
kernel |
A |
h |
A single positive |
censorH |
A single positive |
na.rm |
If |
robust |
If |
... |
Not used. |
verbose |
See |
Returns a numeric
KxI matrix
(or a vector
of length K).
Henrik Bengtsson
J <- 100 I <- 4 Y <- matrix(rnorm(I*J, sd=1/2), ncol=I) # Introduce a gain in column 2 and 3 Y[30:50,2:3] <- Y[30:50,2:3] + 3 x <- 1:J xOut <- x Ys1 <- colKernelSmoothing(Y, x=x, xOut=xOut, kernel="gaussian", h=1) Ys5 <- colKernelSmoothing(Y, x=x, xOut=xOut, kernel="gaussian", h=5) xlim <- range(c(x,xOut)) ylim <- c(-3,5) layout(matrix(1:I, ncol=1)) par(mar=c(3,3,1,1)+0.1, pch=19) for (ii in 1:I) { plot(NA, xlim=xlim, ylim=ylim) points(x, Y[,ii], col="#999999") lines(xOut, Ys1[,ii], col=2) points(xOut, Ys1[,ii], col=2) lines(xOut, Ys5[,ii], col=3) points(xOut, Ys5[,ii], col=3) }
J <- 100 I <- 4 Y <- matrix(rnorm(I*J, sd=1/2), ncol=I) # Introduce a gain in column 2 and 3 Y[30:50,2:3] <- Y[30:50,2:3] + 3 x <- 1:J xOut <- x Ys1 <- colKernelSmoothing(Y, x=x, xOut=xOut, kernel="gaussian", h=1) Ys5 <- colKernelSmoothing(Y, x=x, xOut=xOut, kernel="gaussian", h=5) xlim <- range(c(x,xOut)) ylim <- c(-3,5) layout(matrix(1:I, ncol=1)) par(mar=c(3,3,1,1)+0.1, pch=19) for (ii in 1:I) { plot(NA, xlim=xlim, ylim=ylim) points(x, Y[,ii], col="#999999") lines(xOut, Ys1[,ii], col=2) points(xOut, Ys1[,ii], col=2) lines(xOut, Ys5[,ii], col=3) points(xOut, Ys5[,ii], col=3) }
Package: aroma.core
Class CopyNumberChromosomalModel
Object
~~|
~~+--
ChromosomalModel
~~~~~~~|
~~~~~~~+--
CopyNumberChromosomalModel
Directly known subclasses:
CbsModel, CopyNumberSegmentationModel, GladModel, HaarSegModel, RawCopyNumberModel
public abstract static class CopyNumberChromosomalModel
extends ChromosomalModel
This abstract class represents a copy-number model.
CopyNumberChromosomalModel(cesTuple=NULL, refTuple=NULL, calculateRatios=TRUE, tags="*", genome="Human", chromosomes=NULL, maxNAFraction=1/5, ...)
CopyNumberChromosomalModel(cesTuple=NULL, refTuple=NULL, calculateRatios=TRUE, tags="*", genome="Human", chromosomes=NULL, maxNAFraction=1/5, ...)
cesTuple |
|
refTuple |
An optional |
calculateRatios |
A |
tags |
|
genome |
A |
chromosomes |
(optional) A |
maxNAFraction |
A |
... |
Optional arguments that may be used by some of the subclass models. |
Methods:
extractRawCopyNumbers |
Extracts relative copy numbers. | |
fit |
Fits the model. | |
getChromosomeLength |
- | |
getNames |
- | |
getReference |
- | |
isPaired |
- | |
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
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
This class requires genome information annotation files for every chip type.
Henrik Bengtsson
Package: aroma.core
Class CopyNumberSegmentationModel
Object
~~|
~~+--
ChromosomalModel
~~~~~~~|
~~~~~~~+--
CopyNumberChromosomalModel
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
CopyNumberSegmentationModel
Directly known subclasses:
CbsModel, GladModel, HaarSegModel
public abstract static class CopyNumberSegmentationModel
extends CopyNumberChromosomalModel
This abstract class represents a copy-number segmentation model.
CopyNumberSegmentationModel(...)
CopyNumberSegmentationModel(...)
... |
Arguments passed to constructor
|
Methods:
fit |
Fits the model. | |
getFullNames |
- | |
getRegions |
- | |
getTags |
- | |
plot |
- | |
writeRegions |
- | |
Methods inherited from CopyNumberChromosomalModel:
as.character, calculateChromosomeStatistics, calculateRatios, estimateSds, extractRawCopyNumbers, fit, getChromosomeLength, getDataFileMatrix, getMaxNAFraction, getNames, getOptionalArguments, getPairedNames, getRefSetTuple, getReference, getReferenceSetTuple, isPaired, newPlot, plotAxesLayers, plotChromosomesLayers, plotCytobandLayers, plotFitLayers, plotGridHorizontalLayers, plotRawCopyNumbers, plotSampleLayers, setReference
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
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Performs Circular Binary Segmentation (CBS) on a data set for one or more chip types.
## Default S3 method: doCBS(dataSet, tags=NULL, chipTypes, arrays=NULL, ..., verbose=FALSE) ## S3 method for class 'CopyNumberDataSet' doCBS(ds, arrays=NULL, ...) ## S3 method for class 'CopyNumberDataSetTuple' doCBS(dsTuple, arrays=NULL, ..., verbose=FALSE)
## Default S3 method: doCBS(dataSet, tags=NULL, chipTypes, arrays=NULL, ..., verbose=FALSE) ## S3 method for class 'CopyNumberDataSet' doCBS(ds, arrays=NULL, ...) ## S3 method for class 'CopyNumberDataSetTuple' doCBS(dsTuple, arrays=NULL, ..., verbose=FALSE)
ds , dsTuple , dataSet
|
A |
tags |
An optional |
chipTypes |
A |
arrays |
An optional |
... |
Additional arguments passed to |
verbose |
Returns the output dataset of CbsModel
.
Henrik Bengtsson
## Not run: dataSet <- "GSE20939" tags <- "ACC,-XY,BPN,-XY,RMA,FLN,-XY" chipTypes <- c("Mapping250K_Nsp", "Mapping250K_Sty") fit <- doCBS(dataSet, tags=tags, chipTypes=chipTypes, verbose=-10) print(fit) ## End(Not run)
## Not run: dataSet <- "GSE20939" tags <- "ACC,-XY,BPN,-XY,RMA,FLN,-XY" chipTypes <- c("Mapping250K_Nsp", "Mapping250K_Sty") fit <- doCBS(dataSet, tags=tags, chipTypes=chipTypes, verbose=-10) print(fit) ## End(Not run)
Package: aroma.core
Class Explorer
Object
~~|
~~+--
Explorer
Directly known subclasses:
ChromosomeExplorer
public abstract static class Explorer
extends Object
Explorer(tags="*", version="0", ...)
Explorer(tags="*", version="0", ...)
tags |
|
version |
An optional |
... |
Not used. |
Methods:
display |
Displays the explorer in the default browser. | |
getFullName |
- | |
getName |
Gets the name of the explorer. | |
getNames |
Gets the names of the input samples. | |
getPath |
Gets the path of the output directory. | |
getRootPath |
Gets the root path of the output directory. | |
getTags |
Gets the tags of the explorer. | |
getVersion |
- | |
nbrOfArrays |
Gets the total number of arrays. | |
process |
Generates image files, scripts and dynamic pages for the explorer. | |
setArrays |
Sets the arrays. | |
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
The main directory of an Explorer report is
reports/<name>/<subname>/
.
The <name>
is typically the same as the name of the input
data set, and the <subname>
is typically the tags of ditto.
This main directory is where main HTML document is stored.
For each chip type, real or "virtual" (combined), there is a
subdirectory with the same name as the chip type, i.e.
reports/<name>/<subname>/<chiptype>/
.
For each chip type directory, there are set of subdirectories each
specifying a so called image layer, e.g. an image layer
showing the raw data, another containing the estimates of a model
fit and so on. Path format:
reports/<name>/<subname>/<chiptype>/<image layer>/
.
In this directory all image files are stored, e.g. PNG files.
In some cases one do not want to all input tags to become part of the subname, but instead for instance use those to name the image layer(s). In such cases one has to override the default names.
Henrik Bengtsson
Package: aroma.core
Class GladModel
Object
~~|
~~+--
ChromosomalModel
~~~~~~~|
~~~~~~~+--
CopyNumberChromosomalModel
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
CopyNumberSegmentationModel
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
GladModel
Directly known subclasses:
public static class GladModel
extends CopyNumberSegmentationModel
This class represents the Gain and Loss Analysis of DNA regions (GLAD) model [1]. This class can model chip-effect estimates obtained from multiple chip types, and not all samples have to be available on all chip types.
GladModel(cesTuple=NULL, ...)
GladModel(cesTuple=NULL, ...)
cesTuple |
|
... |
Arguments passed to the constructor of
|
Data from multiple chip types are combined "as is". This is based on the assumption that the relative chip effect estimates are non-biased (or at the equally biased across chip types). Note that in GLAD there is no way to down weight certain data points, which is why we can control for differences in variance across chip types.
Methods:
writeRegions |
- | |
Methods inherited from CopyNumberSegmentationModel:
fit, getAsteriskTags, getFitFunction, getFullNames, getRegions, getTags, plot, plotCopyNumberRegionLayers, writeRegions
Methods inherited from CopyNumberChromosomalModel:
as.character, calculateChromosomeStatistics, calculateRatios, estimateSds, extractRawCopyNumbers, fit, getChromosomeLength, getDataFileMatrix, getMaxNAFraction, getNames, getOptionalArguments, getPairedNames, getRefSetTuple, getReference, getReferenceSetTuple, isPaired, newPlot, plotAxesLayers, plotChromosomesLayers, plotCytobandLayers, plotFitLayers, plotGridHorizontalLayers, plotRawCopyNumbers, plotSampleLayers, setReference
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
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
In high-density copy numbers analysis, the most time consuming step is fitting the GLAD model. The complexity of the model grows more than linearly (squared? exponentially?) with the number of data points in the chromosome and sample being fitted. This is why it take much more than twice the time to fit two chip types together than separately.
Henrik Bengtsson
[1] Hupe P et al. Analysis of array CGH data: from signal ratio to
gain and loss of DNA regions. Bioinformatics, 2004, 20, 3413-3422.
Package: aroma.core
Class HaarSegModel
Object
~~|
~~+--
ChromosomalModel
~~~~~~~|
~~~~~~~+--
CopyNumberChromosomalModel
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
CopyNumberSegmentationModel
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
HaarSegModel
Directly known subclasses:
public static class HaarSegModel
extends CopyNumberSegmentationModel
This class represents the Haar wavelet-based segmentation (HaarSeg) model [1].
HaarSegModel(cesTuple=NULL, ..., breaksFdrQ=1e-04)
HaarSegModel(cesTuple=NULL, ..., breaksFdrQ=1e-04)
cesTuple |
|
breaksFdrQ |
Default tuning parameters specific to the HaarSeg algorithm. |
... |
Arguments passed to the constructor of
|
Methods:
No methods defined.
Methods inherited from CopyNumberSegmentationModel:
fit, getAsteriskTags, getFitFunction, getFullNames, getRegions, getTags, plot, plotCopyNumberRegionLayers, writeRegions
Methods inherited from CopyNumberChromosomalModel:
as.character, calculateChromosomeStatistics, calculateRatios, estimateSds, extractRawCopyNumbers, fit, getChromosomeLength, getDataFileMatrix, getMaxNAFraction, getNames, getOptionalArguments, getPairedNames, getRefSetTuple, getReference, getReferenceSetTuple, isPaired, newPlot, plotAxesLayers, plotChromosomesLayers, plotCytobandLayers, plotFitLayers, plotGridHorizontalLayers, plotRawCopyNumbers, plotSampleLayers, setReference
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
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
[1] Ben-Yaacov E. and Eldar YC. A fast and flexible method for the segmentation of aCGH data, Bioinformatics, 2008. https://webee.technion.ac.il/Sites/People/YoninaEldar/software_det1.php
Package: aroma.core
Class NonPairedPSCNData
data.frame
~~|
~~+--
RichDataFrame
~~~~~~~|
~~~~~~~+--
RawGenomicSignals
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
AbstractCNData
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
AbstractPSCNData
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
NonPairedPSCNData
Directly known subclasses:
public class NonPairedPSCNData
extends AbstractPSCNData
A NonPairedPSCNData object holds parent-specific copy number data.
Two NonPairedPSCNData objects for a matched tumor-normal pair can
be combined into a PairedPSCNData
object.
NonPairedPSCNData(chromosome=NULL, x=NULL, isSNP=NULL, mu=NULL, C=NULL, beta=NULL, ...)
NonPairedPSCNData(chromosome=NULL, x=NULL, isSNP=NULL, mu=NULL, C=NULL, beta=NULL, ...)
C |
A |
beta |
A |
mu |
An optional |
isSNP |
An optional |
chromosome |
(Optional) An |
x |
Optional |
... |
Optional named locus-specific signal |
Methods:
as |
- | |
as.NonPairedPSCNData |
- | |
as.PairedPSCNData |
- | |
callNaiveGenotypes |
- | |
callSegmentationOutliers |
- | |
dropSegmentationOutliers |
- | |
getSignalColumnNames |
- | |
segmentByCBS |
- | |
Methods inherited from AbstractPSCNData:
callSNPs, getSNPFields
Methods inherited from AbstractCNData:
findLargeGaps, getChipType, getLocusData, getPlatform, hasKnownPositions, orderAlongGenome, setChipType, setPlatform
Methods inherited from RawGenomicSignals:
*, +, -, addBy, append, applyBinaryOperator, as.character, as.data.frame, assertOneChromosome, binnedSmoothing, binnedSmoothingByField, clearCache, clone, divideBy, drawDensity, estimateStandardDeviation, extractChromosome, extractChromosomes, extractDataForSegmentation, extractRegion, extractRegions, extractSubset, gaussianSmoothing, getBasicField, getCXY, getChromosome, getChromosomes, getDefaultLocusFields, getLocusFields, getPositions, getSigma, getSignalColumnName, getSignalColumnNames, getSignals, getWeights, getXScale, getXY, getYScale, hasWeights, kernelSmoothing, lines, multiplyBy, nbrOfChromosomes, nbrOfLoci, plot, points, print, segmentByCBS, segmentByGLAD, segmentByHaarSeg, segmentByMPCBS, setBasicField, setSigma, setSignals, setWeights, setXScale, setYScale, signalRange, sort, subtractBy, xMax, xMin, xRange, xSeq, yMax, yMin, yRange
Methods inherited from RichDataFrame:
$, $<-, [, [[, [[<-, as.data.frame, as.list, dim, dropVirtualColumn, getColumnNames, getColumnNamesTranslator, getFullName, getName, getTags, getVirtualColumn, getVirtualColumnFunction, getVirtualColumnNames, hasColumn, hasColumns, hasVirtualColumn, hasVirtualColumns, length, names, newInstance, print, rbind, setAttributes, setColumnNamesMap, setColumnNamesTranslator, setName, setTags, setVirtualColumn, subset, translateColumnNames
Methods inherited from data.frame:
$<-,data.frame-method, $<-, Math, Ops,nonStructure,vector-method, Ops,structure,vector-method, Ops,vector,nonStructure-method, Ops,vector,structure-method, Ops, Summary, [, [<-,data.frame-method, [<-, [[, [[<-,data.frame-method, [[<-, aggregate, anyDuplicated, anyNA, as.NonPairedPSCNData, as.PairedPSCNData, as.data.frame, as.list, as.matrix, as.vector, attachLocally, by, callSegmentationOutliers, cbind, coerce,ANY,list-method, coerce,oldClass,S3-method, dim, dimnames, dimnames<-, dropSegmentationOutliers, droplevels, duplicated, edit, findLargeGaps, format, formula, head, initialize,oldClass-method, is.na, merge, na.exclude, na.omit, plot, plotDensity, print, prompt, rbind, row.names, row.names<-, rowsum, segmentByCBS, segmentByPairedPSCBS, show,oldClass-method, slotsFromS3,data.frame-method, split, split<-, stack, str, subset, summary, t, tail, transform, type.convert, unique, unstack, unwrap, within, wrap, writeDataFrame, xtfrm
Henrik Bengtsson
Package: aroma.core
Class PairedPSCNData
data.frame
~~|
~~+--
RichDataFrame
~~~~~~~|
~~~~~~~+--
RawGenomicSignals
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
AbstractCNData
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
AbstractPSCNData
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
PairedPSCNData
Directly known subclasses:
public class PairedPSCNData
extends AbstractPSCNData
A PairedPSCNData object holds paired tumor-normal parent-specific copy number data.
PairedPSCNData(chromosome=NULL, x=NULL, isSNP=NULL, muN=NULL, CT=NULL, betaT=NULL, CN=NULL, betaN=NULL, ...)
PairedPSCNData(chromosome=NULL, x=NULL, isSNP=NULL, muN=NULL, CT=NULL, betaT=NULL, CN=NULL, betaN=NULL, ...)
CT |
A |
CN |
|
betaT |
A |
betaN |
A |
muN |
An optional |
isSNP |
An optional |
chromosome |
(Optional) An |
x |
Optional |
... |
Optional named locus-specific signal |
Methods:
as |
- | |
as.PairedPSCNData |
- | |
callNaiveGenotypes |
- | |
callSegmentationOutliers |
- | |
dropSegmentationOutliers |
- | |
getSignalColumnNames |
- | |
getTCNs |
- | |
getTotalCopyNumbers |
- | |
normalizeTumorBoost |
- | |
plotTracks |
- | |
segmentByCBS |
- | |
segmentByPairedPSCBS |
- | |
Methods inherited from AbstractPSCNData:
callSNPs, getSNPFields
Methods inherited from AbstractCNData:
findLargeGaps, getChipType, getLocusData, getPlatform, hasKnownPositions, orderAlongGenome, setChipType, setPlatform
Methods inherited from RawGenomicSignals:
*, +, -, addBy, append, applyBinaryOperator, as.character, as.data.frame, assertOneChromosome, binnedSmoothing, binnedSmoothingByField, clearCache, clone, divideBy, drawDensity, estimateStandardDeviation, extractChromosome, extractChromosomes, extractDataForSegmentation, extractRegion, extractRegions, extractSubset, gaussianSmoothing, getBasicField, getCXY, getChromosome, getChromosomes, getDefaultLocusFields, getLocusFields, getPositions, getSigma, getSignalColumnName, getSignalColumnNames, getSignals, getWeights, getXScale, getXY, getYScale, hasWeights, kernelSmoothing, lines, multiplyBy, nbrOfChromosomes, nbrOfLoci, plot, points, print, segmentByCBS, segmentByGLAD, segmentByHaarSeg, segmentByMPCBS, setBasicField, setSigma, setSignals, setWeights, setXScale, setYScale, signalRange, sort, subtractBy, xMax, xMin, xRange, xSeq, yMax, yMin, yRange
Methods inherited from RichDataFrame:
$, $<-, [, [[, [[<-, as.data.frame, as.list, dim, dropVirtualColumn, getColumnNames, getColumnNamesTranslator, getFullName, getName, getTags, getVirtualColumn, getVirtualColumnFunction, getVirtualColumnNames, hasColumn, hasColumns, hasVirtualColumn, hasVirtualColumns, length, names, newInstance, print, rbind, setAttributes, setColumnNamesMap, setColumnNamesTranslator, setName, setTags, setVirtualColumn, subset, translateColumnNames
Methods inherited from data.frame:
$<-,data.frame-method, $<-, Math, Ops,nonStructure,vector-method, Ops,structure,vector-method, Ops,vector,nonStructure-method, Ops,vector,structure-method, Ops, Summary, [, [<-,data.frame-method, [<-, [[, [[<-,data.frame-method, [[<-, aggregate, anyDuplicated, anyNA, as.NonPairedPSCNData, as.PairedPSCNData, as.data.frame, as.list, as.matrix, as.vector, attachLocally, by, callSegmentationOutliers, cbind, coerce,ANY,list-method, coerce,oldClass,S3-method, dim, dimnames, dimnames<-, dropSegmentationOutliers, droplevels, duplicated, edit, findLargeGaps, format, formula, head, initialize,oldClass-method, is.na, merge, na.exclude, na.omit, plot, plotDensity, print, prompt, rbind, row.names, row.names<-, rowsum, segmentByCBS, segmentByPairedPSCBS, show,oldClass-method, slotsFromS3,data.frame-method, split, split<-, stack, str, subset, summary, t, tail, transform, type.convert, unique, unstack, unwrap, within, wrap, writeDataFrame, xtfrm
Henrik Bengtsson
Package: aroma.core
Class ParametersInterface
Interface
~~|
~~+--
ParametersInterface
Directly known subclasses:
AromaTransform
public class ParametersInterface
extends Interface
ParametersInterface(...)
ParametersInterface(...)
... |
Not used. |
Methods:
getParameters |
- | |
getParametersAsString |
- | |
Methods inherited from Interface:
extend, print, uses
Henrik Bengtsson
Package: aroma.core
Class RawAlleleBFractions
data.frame
~~|
~~+--
RichDataFrame
~~~~~~~|
~~~~~~~+--
RawGenomicSignals
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
RawAlleleBFractions
Directly known subclasses:
RawMirroredAlleleBFractions, SegmentedAlleleBFractions
public class RawAlleleBFractions
extends RawGenomicSignals
RawAlleleBFractions(...)
RawAlleleBFractions(...)
... |
Arguments passed to |
Methods:
extractRawMirroredAlleleBFractions |
- | |
plot |
- | |
Methods inherited from RawGenomicSignals:
*, +, -, addBy, append, applyBinaryOperator, as.character, as.data.frame, assertOneChromosome, binnedSmoothing, binnedSmoothingByField, clearCache, clone, divideBy, drawDensity, estimateStandardDeviation, extractChromosome, extractChromosomes, extractDataForSegmentation, extractRegion, extractRegions, extractSubset, gaussianSmoothing, getBasicField, getCXY, getChromosome, getChromosomes, getDefaultLocusFields, getLocusFields, getPositions, getSigma, getSignalColumnName, getSignalColumnNames, getSignals, getWeights, getXScale, getXY, getYScale, hasWeights, kernelSmoothing, lines, multiplyBy, nbrOfChromosomes, nbrOfLoci, plot, points, print, segmentByCBS, segmentByGLAD, segmentByHaarSeg, segmentByMPCBS, setBasicField, setSigma, setSignals, setWeights, setXScale, setYScale, signalRange, sort, subtractBy, xMax, xMin, xRange, xSeq, yMax, yMin, yRange
Methods inherited from RichDataFrame:
$, $<-, [, [[, [[<-, as.data.frame, as.list, dim, dropVirtualColumn, getColumnNames, getColumnNamesTranslator, getFullName, getName, getTags, getVirtualColumn, getVirtualColumnFunction, getVirtualColumnNames, hasColumn, hasColumns, hasVirtualColumn, hasVirtualColumns, length, names, newInstance, print, rbind, setAttributes, setColumnNamesMap, setColumnNamesTranslator, setName, setTags, setVirtualColumn, subset, translateColumnNames
Methods inherited from data.frame:
$<-,data.frame-method, $<-, Math, Ops,nonStructure,vector-method, Ops,structure,vector-method, Ops,vector,nonStructure-method, Ops,vector,structure-method, Ops, Summary, [, [<-,data.frame-method, [<-, [[, [[<-,data.frame-method, [[<-, aggregate, anyDuplicated, anyNA, as.NonPairedPSCNData, as.PairedPSCNData, as.data.frame, as.list, as.matrix, as.vector, attachLocally, by, callSegmentationOutliers, cbind, coerce,ANY,list-method, coerce,oldClass,S3-method, dim, dimnames, dimnames<-, dropSegmentationOutliers, droplevels, duplicated, edit, findLargeGaps, format, formula, head, initialize,oldClass-method, is.na, merge, na.exclude, na.omit, plot, plotDensity, print, prompt, rbind, row.names, row.names<-, rowsum, segmentByCBS, segmentByPairedPSCBS, show,oldClass-method, slotsFromS3,data.frame-method, split, split<-, stack, str, subset, summary, t, tail, transform, type.convert, unique, unstack, unwrap, within, wrap, writeDataFrame, xtfrm
Henrik Bengtsson
Package: aroma.core
Class RawCopyNumberModel
Object
~~|
~~+--
ChromosomalModel
~~~~~~~|
~~~~~~~+--
CopyNumberChromosomalModel
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
RawCopyNumberModel
Directly known subclasses:
public abstract static class RawCopyNumberModel
extends CopyNumberChromosomalModel
This class represents an identity copy-number model which returns the input as is.
RawCopyNumberModel(...)
RawCopyNumberModel(...)
... |
Passed to the constructor of the superclass. |
Methods:
No methods defined.
Methods inherited from CopyNumberChromosomalModel:
as.character, calculateChromosomeStatistics, calculateRatios, estimateSds, extractRawCopyNumbers, fit, getChromosomeLength, getDataFileMatrix, getMaxNAFraction, getNames, getOptionalArguments, getPairedNames, getRefSetTuple, getReference, getReferenceSetTuple, isPaired, newPlot, plotAxesLayers, plotChromosomesLayers, plotCytobandLayers, plotFitLayers, plotGridHorizontalLayers, plotRawCopyNumbers, plotSampleLayers, setReference
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
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson
Package: aroma.core
Class RawCopyNumbers
data.frame
~~|
~~+--
RichDataFrame
~~~~~~~|
~~~~~~~+--
RawGenomicSignals
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
RawCopyNumbers
Directly known subclasses:
SegmentedCopyNumbers
public class RawCopyNumbers
extends RawGenomicSignals
RawCopyNumbers(cn=NULL, ...)
RawCopyNumbers(cn=NULL, ...)
cn |
A |
... |
Arguments passed to |
Methods:
cnRange |
- | |
extractRawCopyNumbers |
- | |
getSignals |
- | |
plot |
- | |
Methods inherited from RawGenomicSignals:
*, +, -, addBy, append, applyBinaryOperator, as.character, as.data.frame, assertOneChromosome, binnedSmoothing, binnedSmoothingByField, clearCache, clone, divideBy, drawDensity, estimateStandardDeviation, extractChromosome, extractChromosomes, extractDataForSegmentation, extractRegion, extractRegions, extractSubset, gaussianSmoothing, getBasicField, getCXY, getChromosome, getChromosomes, getDefaultLocusFields, getLocusFields, getPositions, getSigma, getSignalColumnName, getSignalColumnNames, getSignals, getWeights, getXScale, getXY, getYScale, hasWeights, kernelSmoothing, lines, multiplyBy, nbrOfChromosomes, nbrOfLoci, plot, points, print, segmentByCBS, segmentByGLAD, segmentByHaarSeg, segmentByMPCBS, setBasicField, setSigma, setSignals, setWeights, setXScale, setYScale, signalRange, sort, subtractBy, xMax, xMin, xRange, xSeq, yMax, yMin, yRange
Methods inherited from RichDataFrame:
$, $<-, [, [[, [[<-, as.data.frame, as.list, dim, dropVirtualColumn, getColumnNames, getColumnNamesTranslator, getFullName, getName, getTags, getVirtualColumn, getVirtualColumnFunction, getVirtualColumnNames, hasColumn, hasColumns, hasVirtualColumn, hasVirtualColumns, length, names, newInstance, print, rbind, setAttributes, setColumnNamesMap, setColumnNamesTranslator, setName, setTags, setVirtualColumn, subset, translateColumnNames
Methods inherited from data.frame:
$<-,data.frame-method, $<-, Math, Ops,nonStructure,vector-method, Ops,structure,vector-method, Ops,vector,nonStructure-method, Ops,vector,structure-method, Ops, Summary, [, [<-,data.frame-method, [<-, [[, [[<-,data.frame-method, [[<-, aggregate, anyDuplicated, anyNA, as.NonPairedPSCNData, as.PairedPSCNData, as.data.frame, as.list, as.matrix, as.vector, attachLocally, by, callSegmentationOutliers, cbind, coerce,ANY,list-method, coerce,oldClass,S3-method, dim, dimnames, dimnames<-, dropSegmentationOutliers, droplevels, duplicated, edit, findLargeGaps, format, formula, head, initialize,oldClass-method, is.na, merge, na.exclude, na.omit, plot, plotDensity, print, prompt, rbind, row.names, row.names<-, rowsum, segmentByCBS, segmentByPairedPSCBS, show,oldClass-method, slotsFromS3,data.frame-method, split, split<-, stack, str, subset, summary, t, tail, transform, type.convert, unique, unstack, unwrap, within, wrap, writeDataFrame, xtfrm
Henrik Bengtsson
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Simulating copy-number data # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Number of loci J <- 1000 mu <- double(J) mu[200:300] <- mu[200:300] + 1 mu[650:800] <- mu[650:800] - 1 eps <- rnorm(J, sd=1/2) y <- mu + eps x <- sort(runif(length(y), max=length(y))) cn <- RawCopyNumbers(y, x) print(cn) cn2 <- extractSubset(cn, subset=xSeq(cn, by=5)) print(cn2) # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Plot along genome # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - plot(cn, ylim=c(-3,3)) title(main="Complete and subsetted loci") points(cn2, col="red", pch=176, cex=2) legend("topright", pch=c(19,176), col=c("#999999", "red"), sprintf(c("raw [n=%d]", "every 5th [n=%d]"), c(nbrOfLoci(cn), nbrOfLoci(cn2))), bty="n") # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Binned smoothing # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - plot(cn, col="#999999", ylim=c(-3,3)) title(main="Binned smoothing") cnSa <- binnedSmoothing(cn, by=3) lines(cnSa, col="blue") points(cnSa, col="blue") cnSb <- binnedSmoothing(cn, by=9) lines(cnSb, col="red") points(cnSb, col="red") legend("topright", pch=19, col=c("#999999", "blue", "red"), sprintf(c("raw [n=%d]", "Bin(w=3) [n=%d]", "Bin(w=9) [n=%d]"), c(nbrOfLoci(cn), nbrOfLoci(cnSa), nbrOfLoci(cnSb))), bty="n") # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Binned smoothing (by count) # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - plot(cn, col="#999999", ylim=c(-3,3)) title(main="Binned smoothing (by count)") cnSa <- binnedSmoothing(cn, by=3, byCount=TRUE) lines(cnSa, col="blue") points(cnSa, col="blue") cnSb <- binnedSmoothing(cn, by=9, byCount=TRUE) lines(cnSb, col="red") points(cnSb, col="red") legend("topright", pch=19, col=c("#999999", "blue", "red"), sprintf(c("raw [n=%d]", "BinO(w=3) [n=%d]", "BinO(w=9) [n=%d]"), c(nbrOfLoci(cn), nbrOfLoci(cnSa), nbrOfLoci(cnSb))), bty="n") # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Kernel smoothing (default is Gaussian) # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - plot(cn, col="#999999", ylim=c(-3,3)) title(main="Kernel smoothing w/ Gaussian kernel") cnSa <- kernelSmoothing(cn, h=2) points(cnSa, col="blue") cnSb <- kernelSmoothing(cn, h=5) points(cnSb, col="red") legend("topright", pch=19, col=c("#999999", "blue", "red"), sprintf(c("raw [n=%d]", "N(.,sd=2) [n=%d]", "N(.,sd=5) [n=%d]"), c(nbrOfLoci(cn), nbrOfLoci(cnSa), nbrOfLoci(cnSb))), bty="n") # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Kernel smoothing # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - plot(cn, col="#999999", ylim=c(-3,3)) title(main="Kernel smoothing w/ uniform kernel") xOut <- xSeq(cn, by=10) cnSa <- kernelSmoothing(cn, xOut=xOut, kernel="uniform", h=2) lines(cnSa, col="blue") points(cnSa, col="blue") cnSb <- kernelSmoothing(cn, xOut=xOut, kernel="uniform", h=5) lines(cnSb, col="red") points(cnSb, col="red") legend("topright", pch=19, col=c("#999999", "blue", "red"), sprintf(c("raw [n=%d]", "U(w=2) [n=%d]", "U(w=5) [n=%d]"), c(nbrOfLoci(cn), nbrOfLoci(cnSa), nbrOfLoci(cnSb))), bty="n")
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Simulating copy-number data # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Number of loci J <- 1000 mu <- double(J) mu[200:300] <- mu[200:300] + 1 mu[650:800] <- mu[650:800] - 1 eps <- rnorm(J, sd=1/2) y <- mu + eps x <- sort(runif(length(y), max=length(y))) cn <- RawCopyNumbers(y, x) print(cn) cn2 <- extractSubset(cn, subset=xSeq(cn, by=5)) print(cn2) # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Plot along genome # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - plot(cn, ylim=c(-3,3)) title(main="Complete and subsetted loci") points(cn2, col="red", pch=176, cex=2) legend("topright", pch=c(19,176), col=c("#999999", "red"), sprintf(c("raw [n=%d]", "every 5th [n=%d]"), c(nbrOfLoci(cn), nbrOfLoci(cn2))), bty="n") # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Binned smoothing # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - plot(cn, col="#999999", ylim=c(-3,3)) title(main="Binned smoothing") cnSa <- binnedSmoothing(cn, by=3) lines(cnSa, col="blue") points(cnSa, col="blue") cnSb <- binnedSmoothing(cn, by=9) lines(cnSb, col="red") points(cnSb, col="red") legend("topright", pch=19, col=c("#999999", "blue", "red"), sprintf(c("raw [n=%d]", "Bin(w=3) [n=%d]", "Bin(w=9) [n=%d]"), c(nbrOfLoci(cn), nbrOfLoci(cnSa), nbrOfLoci(cnSb))), bty="n") # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Binned smoothing (by count) # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - plot(cn, col="#999999", ylim=c(-3,3)) title(main="Binned smoothing (by count)") cnSa <- binnedSmoothing(cn, by=3, byCount=TRUE) lines(cnSa, col="blue") points(cnSa, col="blue") cnSb <- binnedSmoothing(cn, by=9, byCount=TRUE) lines(cnSb, col="red") points(cnSb, col="red") legend("topright", pch=19, col=c("#999999", "blue", "red"), sprintf(c("raw [n=%d]", "BinO(w=3) [n=%d]", "BinO(w=9) [n=%d]"), c(nbrOfLoci(cn), nbrOfLoci(cnSa), nbrOfLoci(cnSb))), bty="n") # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Kernel smoothing (default is Gaussian) # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - plot(cn, col="#999999", ylim=c(-3,3)) title(main="Kernel smoothing w/ Gaussian kernel") cnSa <- kernelSmoothing(cn, h=2) points(cnSa, col="blue") cnSb <- kernelSmoothing(cn, h=5) points(cnSb, col="red") legend("topright", pch=19, col=c("#999999", "blue", "red"), sprintf(c("raw [n=%d]", "N(.,sd=2) [n=%d]", "N(.,sd=5) [n=%d]"), c(nbrOfLoci(cn), nbrOfLoci(cnSa), nbrOfLoci(cnSb))), bty="n") # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Kernel smoothing # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - plot(cn, col="#999999", ylim=c(-3,3)) title(main="Kernel smoothing w/ uniform kernel") xOut <- xSeq(cn, by=10) cnSa <- kernelSmoothing(cn, xOut=xOut, kernel="uniform", h=2) lines(cnSa, col="blue") points(cnSa, col="blue") cnSb <- kernelSmoothing(cn, xOut=xOut, kernel="uniform", h=5) lines(cnSb, col="red") points(cnSb, col="red") legend("topright", pch=19, col=c("#999999", "blue", "red"), sprintf(c("raw [n=%d]", "U(w=2) [n=%d]", "U(w=5) [n=%d]"), c(nbrOfLoci(cn), nbrOfLoci(cnSa), nbrOfLoci(cnSb))), bty="n")
Package: aroma.core
Class RawGenomicSignals
data.frame
~~|
~~+--
RichDataFrame
~~~~~~~|
~~~~~~~+--
RawGenomicSignals
Directly known subclasses:
AbstractCNData, AbstractPSCNData, NonPairedPSCNData, PairedPSCNData, RawAlleleBFractions, RawCopyNumbers, RawMirroredAlleleBFractions, RawSequenceReads, SegmentedAlleleBFractions, SegmentedCopyNumbers
public class RawGenomicSignals
extends RichDataFrame
RawGenomicSignals(y=NULL, x=NULL, w=NULL, chromosome=0L, name=NULL, ...)
RawGenomicSignals(y=NULL, x=NULL, w=NULL, chromosome=0L, name=NULL, ...)
y |
A |
x |
A (optional) |
w |
A (optional) non-negative |
chromosome |
An (optional) |
name |
An (optional) |
... |
Not used. |
Methods:
* |
- | |
+ |
- | |
- |
- | |
addBy |
- | |
append |
- | |
as.data.frame |
- | |
binnedSmoothing |
- | |
divideBy |
- | |
drawDensity |
- | |
estimateStandardDeviation |
- | |
gaussianSmoothing |
- | |
getChromosome |
- | |
getChromosomes |
- | |
getPositions |
- | |
getSigma |
- | |
getSignals |
- | |
getWeights |
- | |
getXScale |
- | |
getYScale |
- | |
hasWeights |
- | |
kernelSmoothing |
- | |
lines |
- | |
multiplyBy |
- | |
nbrOfChromosomes |
- | |
nbrOfLoci |
- | |
plot |
- | |
points |
- | |
segmentByCBS |
- | |
segmentByGLAD |
- | |
segmentByHaarSeg |
- | |
segmentByMPCBS |
- | |
setSigma |
- | |
setSignals |
- | |
setWeights |
- | |
setXScale |
- | |
setYScale |
- | |
signalRange |
- | |
sort |
- | |
subtractBy |
- | |
xMax |
- | |
xMin |
- | |
xRange |
- | |
xSeq |
- | |
yMax |
- | |
yMin |
- | |
yRange |
- | |
Methods inherited from RichDataFrame:
$, $<-, [, [[, [[<-, as.data.frame, as.list, dim, dropVirtualColumn, getColumnNames, getColumnNamesTranslator, getFullName, getName, getTags, getVirtualColumn, getVirtualColumnFunction, getVirtualColumnNames, hasColumn, hasColumns, hasVirtualColumn, hasVirtualColumns, length, names, newInstance, print, rbind, setAttributes, setColumnNamesMap, setColumnNamesTranslator, setName, setTags, setVirtualColumn, subset, translateColumnNames
Methods inherited from data.frame:
$<-,data.frame-method, $<-, Math, Ops,nonStructure,vector-method, Ops,structure,vector-method, Ops,vector,nonStructure-method, Ops,vector,structure-method, Ops, Summary, [, [<-,data.frame-method, [<-, [[, [[<-,data.frame-method, [[<-, aggregate, anyDuplicated, anyNA, as.NonPairedPSCNData, as.PairedPSCNData, as.data.frame, as.list, as.matrix, as.vector, attachLocally, by, callSegmentationOutliers, cbind, coerce,ANY,list-method, coerce,oldClass,S3-method, dim, dimnames, dimnames<-, dropSegmentationOutliers, droplevels, duplicated, edit, findLargeGaps, format, formula, head, initialize,oldClass-method, is.na, merge, na.exclude, na.omit, plot, plotDensity, print, prompt, rbind, row.names, row.names<-, rowsum, segmentByCBS, segmentByPairedPSCBS, show,oldClass-method, slotsFromS3,data.frame-method, split, split<-, stack, str, subset, summary, t, tail, transform, type.convert, unique, unstack, unwrap, within, wrap, writeDataFrame, xtfrm
Henrik Bengtsson
Package: aroma.core
Class RawMirroredAlleleBFractions
data.frame
~~|
~~+--
RichDataFrame
~~~~~~~|
~~~~~~~+--
RawGenomicSignals
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
RawAlleleBFractions
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
RawMirroredAlleleBFractions
Directly known subclasses:
public class RawMirroredAlleleBFractions
extends RawAlleleBFractions
RawMirroredAlleleBFractions(...)
RawMirroredAlleleBFractions(...)
... |
Arguments passed to |
Methods:
plot |
- | |
Methods inherited from RawAlleleBFractions:
extractRawMirroredAlleleBFractions, plot
Methods inherited from RawGenomicSignals:
*, +, -, addBy, append, applyBinaryOperator, as.character, as.data.frame, assertOneChromosome, binnedSmoothing, binnedSmoothingByField, clearCache, clone, divideBy, drawDensity, estimateStandardDeviation, extractChromosome, extractChromosomes, extractDataForSegmentation, extractRegion, extractRegions, extractSubset, gaussianSmoothing, getBasicField, getCXY, getChromosome, getChromosomes, getDefaultLocusFields, getLocusFields, getPositions, getSigma, getSignalColumnName, getSignalColumnNames, getSignals, getWeights, getXScale, getXY, getYScale, hasWeights, kernelSmoothing, lines, multiplyBy, nbrOfChromosomes, nbrOfLoci, plot, points, print, segmentByCBS, segmentByGLAD, segmentByHaarSeg, segmentByMPCBS, setBasicField, setSigma, setSignals, setWeights, setXScale, setYScale, signalRange, sort, subtractBy, xMax, xMin, xRange, xSeq, yMax, yMin, yRange
Methods inherited from RichDataFrame:
$, $<-, [, [[, [[<-, as.data.frame, as.list, dim, dropVirtualColumn, getColumnNames, getColumnNamesTranslator, getFullName, getName, getTags, getVirtualColumn, getVirtualColumnFunction, getVirtualColumnNames, hasColumn, hasColumns, hasVirtualColumn, hasVirtualColumns, length, names, newInstance, print, rbind, setAttributes, setColumnNamesMap, setColumnNamesTranslator, setName, setTags, setVirtualColumn, subset, translateColumnNames
Methods inherited from data.frame:
$<-,data.frame-method, $<-, Math, Ops,nonStructure,vector-method, Ops,structure,vector-method, Ops,vector,nonStructure-method, Ops,vector,structure-method, Ops, Summary, [, [<-,data.frame-method, [<-, [[, [[<-,data.frame-method, [[<-, aggregate, anyDuplicated, anyNA, as.NonPairedPSCNData, as.PairedPSCNData, as.data.frame, as.list, as.matrix, as.profileCGH, as.vector, attachLocally, by, callSegmentationOutliers, cbind, coerce,ANY,list-method, coerce,oldClass,S3-method, dim, dimnames, dimnames<-, dropSegmentationOutliers, droplevels, duplicated, edit, findLargeGaps, format, formula, head, initialize,oldClass-method, is.na, merge, na.exclude, na.omit, plot, plotDensity, print, prompt, rbind, row.names, row.names<-, rowsum, segmentByCBS, segmentByPairedPSCBS, show,oldClass-method, slotsFromS3,data.frame-method, split, split<-, stack, str, subset, summary, t, tail, transform, type.convert, unique, unstack, unwrap, within, wrap, writeDataFrame, xtfrm
Henrik Bengtsson
Package: aroma.core
Class RawSequenceReads
data.frame
~~|
~~+--
RichDataFrame
~~~~~~~|
~~~~~~~+--
RawGenomicSignals
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
RawSequenceReads
Directly known subclasses:
public class RawSequenceReads
extends RawGenomicSignals
RawSequenceReads(x=NULL, y=rep(1L, length(x)), ...)
RawSequenceReads(x=NULL, y=rep(1L, length(x)), ...)
x |
An |
y |
An (optional) |
... |
Arguments passed to |
Methods:
binnedSums |
- | |
extractRawCopyNumbers |
- | |
nbrOfReads |
- | |
plot |
- | |
Methods inherited from RawGenomicSignals:
*, +, -, addBy, append, applyBinaryOperator, as.character, as.data.frame, assertOneChromosome, binnedSmoothing, binnedSmoothingByField, clearCache, clone, divideBy, drawDensity, estimateStandardDeviation, extractChromosome, extractChromosomes, extractDataForSegmentation, extractRegion, extractRegions, extractSubset, gaussianSmoothing, getBasicField, getCXY, getChromosome, getChromosomes, getDefaultLocusFields, getLocusFields, getPositions, getSigma, getSignalColumnName, getSignalColumnNames, getSignals, getWeights, getXScale, getXY, getYScale, hasWeights, kernelSmoothing, lines, multiplyBy, nbrOfChromosomes, nbrOfLoci, plot, points, print, segmentByCBS, segmentByGLAD, segmentByHaarSeg, segmentByMPCBS, setBasicField, setSigma, setSignals, setWeights, setXScale, setYScale, signalRange, sort, subtractBy, xMax, xMin, xRange, xSeq, yMax, yMin, yRange
Methods inherited from RichDataFrame:
$, $<-, [, [[, [[<-, as.data.frame, as.list, dim, dropVirtualColumn, getColumnNames, getColumnNamesTranslator, getFullName, getName, getTags, getVirtualColumn, getVirtualColumnFunction, getVirtualColumnNames, hasColumn, hasColumns, hasVirtualColumn, hasVirtualColumns, length, names, newInstance, print, rbind, setAttributes, setColumnNamesMap, setColumnNamesTranslator, setName, setTags, setVirtualColumn, subset, translateColumnNames
Methods inherited from data.frame:
$<-,data.frame-method, $<-, Math, Ops,nonStructure,vector-method, Ops,structure,vector-method, Ops,vector,nonStructure-method, Ops,vector,structure-method, Ops, Summary, [, [<-,data.frame-method, [<-, [[, [[<-,data.frame-method, [[<-, aggregate, anyDuplicated, anyNA, as.NonPairedPSCNData, as.PairedPSCNData, as.data.frame, as.list, as.matrix, as.profileCGH, as.vector, attachLocally, by, callSegmentationOutliers, cbind, coerce,ANY,list-method, coerce,oldClass,S3-method, dim, dimnames, dimnames<-, dropSegmentationOutliers, droplevels, duplicated, edit, findLargeGaps, format, formula, head, initialize,oldClass-method, is.na, merge, na.exclude, na.omit, plot, plotDensity, print, prompt, rbind, row.names, row.names<-, rowsum, segmentByCBS, segmentByPairedPSCBS, show,oldClass-method, slotsFromS3,data.frame-method, split, split<-, stack, str, subset, summary, t, tail, transform, type.convert, unique, unstack, unwrap, within, wrap, writeDataFrame, xtfrm
Henrik Bengtsson
Package: aroma.core
Class SegmentedAlleleBFractions
data.frame
~~|
~~+--
RichDataFrame
~~~~~~~|
~~~~~~~+--
RawGenomicSignals
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
RawAlleleBFractions
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
SegmentedGenomicSignalsInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
SegmentedAlleleBFractions
Directly known subclasses:
public class SegmentedAlleleBFractions
extends SegmentedGenomicSignalsInterface
SegmentedAlleleBFractions(..., states=NULL)
SegmentedAlleleBFractions(..., states=NULL)
... |
Arguments passed to |
states |
A |
Methods:
No methods defined.
Methods inherited from SegmentedGenomicSignalsInterface:
as.data.frame, binnedSmoothingByState, extractSubsetByState, findChangePointsByState, getStateColorMap, getStateColors, getStates, getUniqueStates, getVirtualField, getVirtualLocusFields, kernelSmoothingByState, plot, points, setStateColorMap, setStates
Methods inherited from RawAlleleBFractions:
extractRawMirroredAlleleBFractions, plot
Methods inherited from RawGenomicSignals:
*, +, -, addBy, append, applyBinaryOperator, as.character, as.data.frame, assertOneChromosome, binnedSmoothing, binnedSmoothingByField, clearCache, clone, divideBy, drawDensity, estimateStandardDeviation, extractChromosome, extractChromosomes, extractDataForSegmentation, extractRegion, extractRegions, extractSubset, gaussianSmoothing, getBasicField, getCXY, getChromosome, getChromosomes, getDefaultLocusFields, getLocusFields, getPositions, getSigma, getSignalColumnName, getSignalColumnNames, getSignals, getWeights, getXScale, getXY, getYScale, hasWeights, kernelSmoothing, lines, multiplyBy, nbrOfChromosomes, nbrOfLoci, plot, points, print, segmentByCBS, segmentByGLAD, segmentByHaarSeg, segmentByMPCBS, setBasicField, setSigma, setSignals, setWeights, setXScale, setYScale, signalRange, sort, subtractBy, xMax, xMin, xRange, xSeq, yMax, yMin, yRange
Methods inherited from RichDataFrame:
$, $<-, [, [[, [[<-, as.data.frame, as.list, dim, dropVirtualColumn, getColumnNames, getColumnNamesTranslator, getFullName, getName, getTags, getVirtualColumn, getVirtualColumnFunction, getVirtualColumnNames, hasColumn, hasColumns, hasVirtualColumn, hasVirtualColumns, length, names, newInstance, print, rbind, setAttributes, setColumnNamesMap, setColumnNamesTranslator, setName, setTags, setVirtualColumn, subset, translateColumnNames
Methods inherited from data.frame:
$<-,data.frame-method, $<-, Math, Ops,nonStructure,vector-method, Ops,structure,vector-method, Ops,vector,nonStructure-method, Ops,vector,structure-method, Ops, Summary, [, [<-,data.frame-method, [<-, [[, [[<-,data.frame-method, [[<-, aggregate, anyDuplicated, anyNA, as.NonPairedPSCNData, as.PairedPSCNData, as.data.frame, as.list, as.matrix, as.profileCGH, as.vector, attachLocally, by, callSegmentationOutliers, cbind, coerce,ANY,list-method, coerce,oldClass,S3-method, dim, dimnames, dimnames<-, dropSegmentationOutliers, droplevels, duplicated, edit, findLargeGaps, format, formula, head, initialize,oldClass-method, is.na, merge, na.exclude, na.omit, plot, plotDensity, print, prompt, rbind, row.names, row.names<-, rowsum, segmentByCBS, segmentByPairedPSCBS, show,oldClass-method, slotsFromS3,data.frame-method, split, split<-, stack, str, subset, summary, t, tail, transform, type.convert, unique, unstack, unwrap, within, wrap, writeDataFrame, xtfrm
Henrik Bengtsson
Package: aroma.core
Class SegmentedCopyNumbers
data.frame
~~|
~~+--
RichDataFrame
~~~~~~~|
~~~~~~~+--
RawGenomicSignals
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
RawCopyNumbers
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
SegmentedGenomicSignalsInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
SegmentedCopyNumbers
Directly known subclasses:
public class SegmentedCopyNumbers
extends SegmentedGenomicSignalsInterface
SegmentedCopyNumbers(..., states=NULL)
SegmentedCopyNumbers(..., states=NULL)
... |
Arguments passed to |
states |
A |
Methods:
No methods defined.
Methods inherited from SegmentedGenomicSignalsInterface:
as.data.frame, binnedSmoothingByState, extractSubsetByState, findChangePointsByState, getStateColorMap, getStateColors, getStates, getUniqueStates, getVirtualField, getVirtualLocusFields, kernelSmoothingByState, plot, points, setStateColorMap, setStates
Methods inherited from RawCopyNumbers:
cnRange, extractRawCopyNumbers, getCNs, getCn, getSignals, plot
Methods inherited from RawGenomicSignals:
*, +, -, addBy, append, applyBinaryOperator, as.character, as.data.frame, assertOneChromosome, binnedSmoothing, binnedSmoothingByField, clearCache, clone, divideBy, drawDensity, estimateStandardDeviation, extractChromosome, extractChromosomes, extractDataForSegmentation, extractRegion, extractRegions, extractSubset, gaussianSmoothing, getBasicField, getCXY, getChromosome, getChromosomes, getDefaultLocusFields, getLocusFields, getPositions, getSigma, getSignalColumnName, getSignalColumnNames, getSignals, getWeights, getXScale, getXY, getYScale, hasWeights, kernelSmoothing, lines, multiplyBy, nbrOfChromosomes, nbrOfLoci, plot, points, print, segmentByCBS, segmentByGLAD, segmentByHaarSeg, segmentByMPCBS, setBasicField, setSigma, setSignals, setWeights, setXScale, setYScale, signalRange, sort, subtractBy, xMax, xMin, xRange, xSeq, yMax, yMin, yRange
Methods inherited from RichDataFrame:
$, $<-, [, [[, [[<-, as.data.frame, as.list, dim, dropVirtualColumn, getColumnNames, getColumnNamesTranslator, getFullName, getName, getTags, getVirtualColumn, getVirtualColumnFunction, getVirtualColumnNames, hasColumn, hasColumns, hasVirtualColumn, hasVirtualColumns, length, names, newInstance, print, rbind, setAttributes, setColumnNamesMap, setColumnNamesTranslator, setName, setTags, setVirtualColumn, subset, translateColumnNames
Methods inherited from data.frame:
$<-,data.frame-method, $<-, Math, Ops,nonStructure,vector-method, Ops,structure,vector-method, Ops,vector,nonStructure-method, Ops,vector,structure-method, Ops, Summary, [, [<-,data.frame-method, [<-, [[, [[<-,data.frame-method, [[<-, aggregate, anyDuplicated, anyNA, as.NonPairedPSCNData, as.PairedPSCNData, as.data.frame, as.list, as.matrix, as.profileCGH, as.vector, attachLocally, by, callSegmentationOutliers, cbind, coerce,ANY,list-method, coerce,oldClass,S3-method, dim, dimnames, dimnames<-, dropSegmentationOutliers, droplevels, duplicated, edit, findLargeGaps, format, formula, head, initialize,oldClass-method, is.na, merge, na.exclude, na.omit, plot, plotDensity, print, prompt, rbind, row.names, row.names<-, rowsum, segmentByCBS, segmentByPairedPSCBS, show,oldClass-method, slotsFromS3,data.frame-method, split, split<-, stack, str, subset, summary, t, tail, transform, type.convert, unique, unstack, unwrap, within, wrap, writeDataFrame, xtfrm
Henrik Bengtsson
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Simulating copy-number data # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # True CN states stateFcn <- function(x, ...) { states <- integer(length(x)) states[200 <=x & x <= 300] <- -1L states[650 <=x & x <= 800] <- +1L states } # Number of loci J <- 1000 y <- rnorm(J, sd=1/2) x <- 1:length(y) for (state in c(-1,+1)) { idxs <- (stateFcn(x) == state) y[idxs] <- y[idxs] + state } cn <- SegmentedCopyNumbers(y, x, states=stateFcn) print(cn) # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Subsetting # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - plot(cn, ylim=c(-4,4)) title("Copy numbers annotated by state (and subset by state)") cnS <- extractSubsetByState(cn, states=c(0,+1L)) print(cnS) points(cnS, pch=21, cex=1.2, lwd=2, col="purple") legend("topright", pch=c(19, 21), col=c("#999999", "purple"), sprintf(c("raw [n=%d]", "CN in {0,1} [n=%d]"), c(nbrOfLoci(cn), nbrOfLoci(cnS))), bty="n") # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Kernel smoothing stratified by state # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - plot(cn, col="#999999", ylim=c(-3,3)) title(main="Kernel smoothing stratified by state w/ Gaussian kernel") cnSa <- kernelSmoothingByState(cn, h=2) points(cnSa, col="blue") cnSb <- kernelSmoothingByState(cn, h=5) points(cnSb, col="red") legend("topright", pch=19, col=c("#999999", "blue", "red"), sprintf(c("raw [n=%d]", "N(.,sd=2) [n=%d]", "N(.,sd=5) [n=%d]"), c(nbrOfLoci(cn), nbrOfLoci(cnSa), nbrOfLoci(cnSb))), bty="n") # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Binned smoothing stratified by state # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - plot(cn, col="#999999", ylim=c(-3,3)) title(main="Binned smoothing stratified by state") cnSa <- binnedSmoothingByState(cn, by=3, verbose=-1) lines(cnSa, col="blue") points(cnSa, col="blue") cnSb <- binnedSmoothingByState(cn, by=9, verbose=-1) lines(cnSb, col="red") points(cnSb, col="red") legend("topright", pch=19, col=c("#999999", "blue", "red"), sprintf(c("raw [n=%d]", "Bin(w=3) [n=%d]", "Bin(w=9) [n=%d]"), c(nbrOfLoci(cn), nbrOfLoci(cnSa), nbrOfLoci(cnSb))), bty="n")
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Simulating copy-number data # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # True CN states stateFcn <- function(x, ...) { states <- integer(length(x)) states[200 <=x & x <= 300] <- -1L states[650 <=x & x <= 800] <- +1L states } # Number of loci J <- 1000 y <- rnorm(J, sd=1/2) x <- 1:length(y) for (state in c(-1,+1)) { idxs <- (stateFcn(x) == state) y[idxs] <- y[idxs] + state } cn <- SegmentedCopyNumbers(y, x, states=stateFcn) print(cn) # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Subsetting # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - plot(cn, ylim=c(-4,4)) title("Copy numbers annotated by state (and subset by state)") cnS <- extractSubsetByState(cn, states=c(0,+1L)) print(cnS) points(cnS, pch=21, cex=1.2, lwd=2, col="purple") legend("topright", pch=c(19, 21), col=c("#999999", "purple"), sprintf(c("raw [n=%d]", "CN in {0,1} [n=%d]"), c(nbrOfLoci(cn), nbrOfLoci(cnS))), bty="n") # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Kernel smoothing stratified by state # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - plot(cn, col="#999999", ylim=c(-3,3)) title(main="Kernel smoothing stratified by state w/ Gaussian kernel") cnSa <- kernelSmoothingByState(cn, h=2) points(cnSa, col="blue") cnSb <- kernelSmoothingByState(cn, h=5) points(cnSb, col="red") legend("topright", pch=19, col=c("#999999", "blue", "red"), sprintf(c("raw [n=%d]", "N(.,sd=2) [n=%d]", "N(.,sd=5) [n=%d]"), c(nbrOfLoci(cn), nbrOfLoci(cnSa), nbrOfLoci(cnSb))), bty="n") # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Binned smoothing stratified by state # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - plot(cn, col="#999999", ylim=c(-3,3)) title(main="Binned smoothing stratified by state") cnSa <- binnedSmoothingByState(cn, by=3, verbose=-1) lines(cnSa, col="blue") points(cnSa, col="blue") cnSb <- binnedSmoothingByState(cn, by=9, verbose=-1) lines(cnSb, col="red") points(cnSb, col="red") legend("topright", pch=19, col=c("#999999", "blue", "red"), sprintf(c("raw [n=%d]", "Bin(w=3) [n=%d]", "Bin(w=9) [n=%d]"), c(nbrOfLoci(cn), nbrOfLoci(cnSa), nbrOfLoci(cnSb))), bty="n")
Package: aroma.core
Class SegmentedGenomicSignalsInterface
Interface
~~|
~~+--
SegmentedGenomicSignalsInterface
Directly known subclasses:
SegmentedAlleleBFractions, SegmentedCopyNumbers
public class SegmentedGenomicSignalsInterface
extends Interface
SegmentedGenomicSignalsInterface(...)
SegmentedGenomicSignalsInterface(...)
... |
Not used. |
Methods:
as.data.frame |
- | |
binnedSmoothingByState |
- | |
extractSubsetByState |
- | |
findChangePointsByState |
- | |
getStateColorMap |
- | |
getStateColors |
- | |
getStates |
- | |
getUniqueStates |
- | |
kernelSmoothingByState |
- | |
plot |
- | |
points |
- | |
setStateColorMap |
- | |
setStates |
- | |
Methods inherited from Interface:
extend, print, uses
Henrik Bengtsson
Package: aroma.core
Class UnitAnnotationDataFile
Interface
~~|
~~+--
UnitAnnotationDataFile
Directly known subclasses:
AromaUflFile, AromaUgcFile, AromaUgpFile, AromaUnitChromosomeTabularBinaryFile, AromaUnitGcContentFile, AromaUnitTabularBinaryFile, AromaUnitTypesFile, TextUnitNamesFile, UnitNamesFile, UnitTypesFile
public static class UnitAnnotationDataFile
extends Interface
A UnitAnnotationDataFile provides methods for querying certain types of chip type annotation data by units.
UnitAnnotationDataFile(...)
UnitAnnotationDataFile(...)
... |
Arguments passed to |
Methods:
byChipType |
- | |
getAromaUflFile |
- | |
getAromaUgpFile |
- | |
getChipType |
- | |
getPlatform |
- | |
nbrOfUnits |
- | |
Methods inherited from Interface:
extend, print, uses
Henrik Bengtsson
Package: aroma.core
Class UnitNamesFile
Interface
~~|
~~+--
UnitAnnotationDataFile
~~~~~~~|
~~~~~~~+--
UnitNamesFile
Directly known subclasses:
TextUnitNamesFile
public abstract static class UnitNamesFile
extends UnitAnnotationDataFile
A UnitNamesFile provides methods for querying the unit names of a given chip type.
UnitNamesFile(...)
UnitNamesFile(...)
... |
Arguments passed to |
Methods:
getUnitNames |
- | |
indexOf |
- | |
nbrOfUnits |
- | |
Methods inherited from UnitAnnotationDataFile:
byChipType, getAromaUflFile, getAromaUgpFile, getChipType, getDefaultExtension, getPlatform, nbrOfUnits
Methods inherited from Interface:
extend, print, uses
Henrik Bengtsson
Package: aroma.core
Class UnitTypesFile
Interface
~~|
~~+--
UnitAnnotationDataFile
~~~~~~~|
~~~~~~~+--
UnitTypesFile
Directly known subclasses:
AromaUnitTypesFile
public abstract static class UnitTypesFile
extends UnitAnnotationDataFile
A UnitTypesFile provides methods for querying the unit types of a given chip type, e.g. genotyping or copy-number unit, exon unit etc.
UnitTypesFile(...)
UnitTypesFile(...)
... |
Arguments passed to |
Methods:
getUnitTypes |
- | |
nbrOfUnits |
- | |
Methods inherited from UnitAnnotationDataFile:
byChipType, getAromaUflFile, getAromaUgpFile, getChipType, getDefaultExtension, getPlatform, nbrOfUnits
Methods inherited from Interface:
extend, print, uses
unknown=0, expression=1, genotyping=2, resequencing=3, tag=4, copynumber=5, genotypingcontrol=6, expressioncontrol=7
Henrik Bengtsson