aroma.core-package	aroma.core-package
#	Non-documented_objects
$.RichDataFrame	Non-documented_objects
$<-.RichDataFrame	Non-documented_objects
*.CopyNumberRegions	Non-documented_objects
*.RawGenomicSignals	Non-documented_objects
+.CopyNumberRegions	Non-documented_objects
+.RawGenomicSignals	Non-documented_objects
-.CopyNumberRegions	Non-documented_objects
-.RawGenomicSignals	Non-documented_objects
.Machine	Non-documented_objects
/	Non-documented_objects
AbstractCNData	AbstractCNData
AbstractPSCNData	AbstractPSCNData
addBy	Non-documented_objects
addBy.RawGenomicSignals	Non-documented_objects
addIncludes	Non-documented_objects
addIncludes.Explorer	Non-documented_objects
addIndexFile	Non-documented_objects
addIndexFile.ChromosomeExplorer	Non-documented_objects
addIndexFile.Explorer	Non-documented_objects
addLocusFields	Non-documented_objects
addLocusFields.RawGenomicSignals	Non-documented_objects
allocate	Non-documented_objects
allocate,AromaTabularBinaryFile-method	allocate.AromaTabularBinaryFile
allocate.AromaCellCpgFile	Non-documented_objects
allocate.AromaCellPositionFile	Non-documented_objects
allocate.AromaCellSequenceFile	Non-documented_objects
allocate.AromaMicroarrayTabularBinaryFile	Non-documented_objects
allocate.AromaTabularBinaryFile	allocate.AromaTabularBinaryFile
allocate.AromaUflFile	Non-documented_objects
allocate.AromaUgpFile	Non-documented_objects
allocate.AromaUnitCallFile	Non-documented_objects
allocate.AromaUnitChromosomeTabularBinaryFile	Non-documented_objects
allocate.AromaUnitGenotypeCallFile	Non-documented_objects
allocate.AromaUnitPscnBinaryFile	Non-documented_objects
allocate.AromaUnitSignalBinaryFile	Non-documented_objects
allocate.AromaUnitTypesFile	Non-documented_objects
allocateFromUnitAnnotationDataFile	Non-documented_objects
allocateFromUnitAnnotationDataFile.AromaUnitSignalBinaryFile	Non-documented_objects
allocateFromUnitAnnotationDataFile.AromaUnitTabularBinaryFile	Non-documented_objects
allocateFromUnitNamesFile	Non-documented_objects
allocateFromUnitNamesFile.AromaUnitSignalBinaryFile	Non-documented_objects
allocateFromUnitNamesFile.AromaUnitTabularBinaryFile	Non-documented_objects
append	Non-documented_objects
append.CopyNumberRegions	Non-documented_objects
append.RawGenomicSignals	Non-documented_objects
applyBinaryOperator	Non-documented_objects
applyBinaryOperator.RawGenomicSignals	Non-documented_objects
applyRegions	Non-documented_objects
applyRegions.CopyNumberOutliers	Non-documented_objects
applyRows	Non-documented_objects
applyRows.CopyNumberRegions	Non-documented_objects
applyTo	Non-documented_objects
applyTo.SampleAnnotationFile	Non-documented_objects
aroma.core	aroma.core-package
AromaCellCpgFile	AromaCellCpgFile
AromaCellPositionFile	AromaCellPositionFile
AromaCellSequenceFile	Non-documented_objects
AromaCellTabularBinaryFile	AromaCellTabularBinaryFile
AromaCore	Non-documented_objects
AromaGenomeTextFile	AromaGenomeTextFile
AromaMicroarrayDataFile	AromaMicroarrayDataFile
AromaMicroarrayDataSet	AromaMicroarrayDataSet
AromaMicroarrayDataSetTuple	AromaMicroarrayDataSetTuple
AromaMicroarrayDataSetTuple.nbrOfChipTypes	nbrOfChipTypes.AromaMicroarrayDataSetTuple
AromaMicroarrayTabularBinaryFile	AromaMicroarrayTabularBinaryFile
AromaPackage	Non-documented_objects
AromaPlatform	AromaPlatform
AromaPlatformInterface	AromaPlatformInterface
AromaPlatformInterface.getAromaPlatform	getAromaPlatform.AromaPlatformInterface
AromaPlatformInterface.getAromaUflFile	getUnitAnnotationDataFile.AromaPlatformInterface
AromaPlatformInterface.getAromaUgpFile	getUnitAnnotationDataFile.AromaPlatformInterface
AromaPlatformInterface.getChipType	getChipType.AromaPlatformInterface
AromaPlatformInterface.getPlatform	getPlatform.AromaPlatformInterface
AromaPlatformInterface.getUnitAnnotationDataFile	getUnitAnnotationDataFile.AromaPlatformInterface
AromaPlatformInterface.getUnitNamesFile	getUnitAnnotationDataFile.AromaPlatformInterface
AromaPlatformInterface.getUnitTypesFile	getUnitAnnotationDataFile.AromaPlatformInterface
AromaPlatformInterface.isCompatibleWith	isCompatibleWith.AromaPlatformInterface
AromaRepository	AromaRepository
AromaRepository.downloadChipTypeFile	downloadChipTypeFile.AromaRepository
AromaRepository.downloadFile	downloadFile.AromaRepository
AromaRepository.listFiles	listFiles.AromaRepository
AromaSettings	Non-documented_objects
aromaSettings	Non-documented_objects
AromaTabularBinaryFile	AromaTabularBinaryFile
AromaTabularBinaryFile$allocate	allocate.AromaTabularBinaryFile
AromaTabularBinaryFile.allocate	allocate.AromaTabularBinaryFile
AromaTabularBinaryFile.readFooter	readFooter.AromaTabularBinaryFile
AromaTabularBinaryFile.writeFooter	writeFooter.AromaTabularBinaryFile
AromaTabularBinarySet	AromaTabularBinarySet
AromaTransform	AromaTransform
AromaTransform.findFilesTodo	findFilesTodo.AromaTransform
AromaTransform.getFullName	getFullName.AromaTransform
AromaTransform.getInputDataSet	getInputDataSet.AromaTransform
AromaTransform.getName	getName.AromaTransform
AromaTransform.getOutputDataSet	getOutputDataSet.AromaTransform
AromaTransform.getPath	getPath.AromaTransform
AromaTransform.getRootPath	getRootPath.AromaTransform
AromaTransform.getTags	getTags.AromaTransform
AromaTransform.isDone	isDone.AromaTransform
AromaTransform.process	process.AromaTransform
AromaUcscGenomeTextFile	Non-documented_objects
AromaUflFile	Non-documented_objects
AromaUgcFile	Non-documented_objects
AromaUgpFile	Non-documented_objects
AromaUnitCallFile	AromaUnitCallFile
AromaUnitCallSet	AromaUnitCallSet
AromaUnitChromosomeTabularBinaryFile	Non-documented_objects
AromaUnitFracBCnBinaryFile	AromaUnitFracBCnBinaryFile
AromaUnitFracBCnBinarySet	AromaUnitFracBCnBinarySet
AromaUnitGcContentFile	Non-documented_objects
AromaUnitGenotypeCallFile	AromaUnitGenotypeCallFile
AromaUnitGenotypeCallSet	AromaUnitGenotypeCallSet
AromaUnitPscnBinaryFile	AromaUnitPscnBinaryFile
AromaUnitPscnBinarySet	AromaUnitPscnBinarySet
AromaUnitSignalBinaryFile	AromaUnitSignalBinaryFile
AromaUnitSignalBinaryFile.writeDataFrame	writeDataFrame.AromaUnitSignalBinaryFile
AromaUnitSignalBinarySet	AromaUnitSignalBinarySet
AromaUnitSignalBinarySet.writeDataFrame	writeDataFrame.AromaUnitSignalBinarySet
AromaUnitTabularBinaryFile	AromaUnitTabularBinaryFile
AromaUnitTabularBinaryFile.writeDataFrame	writeDataFrame.AromaUnitTabularBinaryFile
AromaUnitTotalCnBinaryFile	AromaUnitTotalCnBinaryFile
AromaUnitTotalCnBinaryFileList	Non-documented_objects
AromaUnitTotalCnBinarySet	AromaUnitTotalCnBinarySet
AromaUnitTotalCnBinarySetTuple	Non-documented_objects
AromaUnitTypesFile	AromaUnitTypesFile
as.AromaMicroarrayDataSetList	Non-documented_objects
as.AromaMicroarrayDataSetList.AromaMicroarrayDataSet	Non-documented_objects
as.AromaMicroarrayDataSetTuple	Non-documented_objects
as.AromaMicroarrayDataSetTuple.AromaMicroarrayDataSet	Non-documented_objects
as.AromaMicroarrayDataSetTuple.AromaMicroarrayDataSetTuple	Non-documented_objects
as.AromaUnitTotalCnBinarySetTuple	Non-documented_objects
as.AromaUnitTotalCnBinarySetTuple.AromaUnitTotalCnBinarySet	Non-documented_objects
as.AromaUnitTotalCnBinarySetTuple.AromaUnitTotalCnBinarySetTuple	Non-documented_objects
as.character.AromaMicroarrayDataSetTuple	Non-documented_objects
as.character.AromaMicroarrayTabularBinaryFile	Non-documented_objects
as.character.AromaPlatform	Non-documented_objects
as.character.AromaTabularBinaryFile	Non-documented_objects
as.character.AromaTransform	Non-documented_objects
as.character.AromaUnitSignalBinaryFile	Non-documented_objects
as.character.ChromosomalModel	Non-documented_objects
as.character.ChromosomeExplorer	Non-documented_objects
as.character.CopyNumberChromosomalModel	Non-documented_objects
as.character.CopyNumberOutliers	Non-documented_objects
as.character.CopyNumberRegions	Non-documented_objects
as.character.Explorer	Non-documented_objects
as.character.RasterImage	Non-documented_objects
as.character.RawGenomicSignals	Non-documented_objects
as.character.SegmentationDataSet	Non-documented_objects
as.character.TextUnitNamesFile	Non-documented_objects
as.CopyNumberDataFile	Non-documented_objects
as.CopyNumberDataFile.CopyNumberDataFile	Non-documented_objects
as.CopyNumberDataSet	Non-documented_objects
as.CopyNumberDataSet.CopyNumberDataSet	Non-documented_objects
as.CopyNumberDataSetTuple	Non-documented_objects
as.CopyNumberDataSetTuple.AromaUnitTotalCnBinarySet	Non-documented_objects
as.CopyNumberDataSetTuple.CopyNumberDataSetTuple	Non-documented_objects
as.CopyNumberDataSetTuple.list	Non-documented_objects
as.data.frame.CopyNumberOutliers	Non-documented_objects
as.data.frame.CopyNumberRegions	Non-documented_objects
as.data.frame.RawCopyNumbers	Non-documented_objects
as.data.frame.RawGenomicSignals	Non-documented_objects
as.data.frame.RichDataFrame	Non-documented_objects
as.data.frame.SegmentedGenomicSignalsInterface	Non-documented_objects
as.GrayscaleImage	Non-documented_objects
as.GrayscaleImage.matrix	as.GrayscaleImage.matrix
as.list.RichDataFrame	Non-documented_objects
as.NonPairedPSCNData	Non-documented_objects
as.NonPairedPSCNData.data.frame	Non-documented_objects
as.NonPairedPSCNData.NonPairedPSCNData	Non-documented_objects
as.PairedPSCNData	Non-documented_objects
as.PairedPSCNData.data.frame	Non-documented_objects
as.PairedPSCNData.NonPairedPSCNData	Non-documented_objects
as.PairedPSCNData.PairedPSCNData	Non-documented_objects
as.TrueColorImage	Non-documented_objects
as.TrueColorImage.Image	Non-documented_objects
as.TrueColorImage.matrix	Non-documented_objects
asMatrixOfFiles	Non-documented_objects
asMatrixOfFiles.AromaMicroarrayDataSetTuple	Non-documented_objects
assertOneChromosome	Non-documented_objects
assertOneChromosome.RawGenomicSignals	Non-documented_objects
asThis	Non-documented_objects
asThis.BasicObject	Non-documented_objects
asThis.Object	Non-documented_objects
backtransformGenotypeCone	Non-documented_objects
backtransformGenotypeCone.matrix	Non-documented_objects
backtransformMultiDimensionalCone	Non-documented_objects
backtransformMultiDimensionalCone.matrix	Non-documented_objects
barSequence	Non-documented_objects
barSequence.ProbePositionEffects	Non-documented_objects
BinnedScatter	BinnedScatter
binnedSmoothing	colBinnedSmoothing.matrix
binnedSmoothing.numeric	colBinnedSmoothing.matrix
binnedSmoothing.RawGenomicSignals	Non-documented_objects
binnedSmoothingByField	Non-documented_objects
binnedSmoothingByField.RawGenomicSignals	Non-documented_objects
binnedSmoothingByState	Non-documented_objects
binnedSmoothingByState.SegmentedGenomicSignalsInterface	Non-documented_objects
binnedSums	Non-documented_objects
binnedSums.RawSequenceReads	Non-documented_objects
binScatter	Non-documented_objects
binScatter.matrix	Non-documented_objects
byChipType	Non-documented_objects
byChipType.AromaCellTabularBinaryFile	Non-documented_objects
byChipType.AromaMicroarrayTabularBinaryFile	Non-documented_objects
byChipType.AromaUnitTabularBinaryFile	Non-documented_objects
byChipType.UnitAnnotationDataFile	Non-documented_objects
byGenome	Non-documented_objects
byGenome.AromaGenomeTextFile	Non-documented_objects
byName.AromaPlatform	Non-documented_objects
byName.AromaUnitFracBCnBinarySet	Non-documented_objects
byName.AromaUnitGenotypeCallSet	Non-documented_objects
byName.AromaUnitPscnBinarySet	Non-documented_objects
byName.AromaUnitSignalBinarySet	Non-documented_objects
byName.AromaUnitTotalCnBinarySet	Non-documented_objects
byName.CbsSegmentationDataSet	Non-documented_objects
byPath.AromaMicroarrayDataSetTuple	Non-documented_objects
byPath.AromaUnitCallSet	Non-documented_objects
byPath.AromaUnitGenotypeCallSet	Non-documented_objects
byPath.CbsSegmentationDataSet	Non-documented_objects
byPath.SegmentationDataSet	Non-documented_objects
byPathnames	Non-documented_objects
byPathnames.SampleAnnotationSet	Non-documented_objects
CacheKeyInterface	CacheKeyInterface
CacheKeyInterface.getCacheKey	getCacheKey.CacheKeyInterface
calcMargins	Non-documented_objects
calcMargins.matrix	Non-documented_objects
calculateAverageColumnAcrossFiles	Non-documented_objects
calculateAverageColumnAcrossFiles.GenericTabularFileSet	Non-documented_objects
calculateChromosomeStatistics	Non-documented_objects
calculateChromosomeStatistics.CopyNumberChromosomalModel	Non-documented_objects
calculateRatios	Non-documented_objects
calculateRatios.CopyNumberChromosomalModel	Non-documented_objects
callNaiveGenotypes	Non-documented_objects
callNaiveGenotypes.NonPairedPSCNData	Non-documented_objects
callNaiveGenotypes.PairedPSCNData	Non-documented_objects
callSegmentationOutliers	Non-documented_objects
callSegmentationOutliers.NonPairedPSCNData	Non-documented_objects
callSegmentationOutliers.PairedPSCNData	Non-documented_objects
callSNPs	Non-documented_objects
callSNPs.AbstractPSCNData	Non-documented_objects
cat	Non-documented_objects
CbsModel	CbsModel
CbsSegmentationDataFile	Non-documented_objects
CbsSegmentationDataSet	Non-documented_objects
ChromosomalModel	ChromosomalModel
ChromosomalModel.getChipType	getChipType.ChromosomalModel
ChromosomalModel.getChromosomes	getChromosomes.ChromosomalModel
ChromosomalModel.getNames	getNames.ChromosomalModel
ChromosomalModel.nbrOfArrays	nbrOfArrays.ChromosomalModel
ChromosomalModel.nbrOfChipTypes	nbrOfChipTypes.ChromosomalModel
ChromosomeExplorer	ChromosomeExplorer
ChromosomeExplorer.getChromosomes	getChromosomes.ChromosomeExplorer
ChromosomeExplorer.getModel	getModel.ChromosomeExplorer
ChromosomeExplorer.process	process.ChromosomeExplorer
ChromosomeExplorer.setArrays	setArrays.ChromosomeExplorer
ChromosomeExplorer.updateSetupExplorerFile	updateSetupExplorerFile.ChromosomeExplorer
clearCache.AromaRepository	Non-documented_objects
clearCache.RawGenomicSignals	Non-documented_objects
clone.RawGenomicSignals	Non-documented_objects
cnRange	Non-documented_objects
cnRange.RawCopyNumbers	Non-documented_objects
colApply	Non-documented_objects
colApply.AromaTabularBinaryFile	Non-documented_objects
colBinnedSmoothing	colBinnedSmoothing.matrix
colBinnedSmoothing.matrix	colBinnedSmoothing.matrix
colGaussianSmoothing	Non-documented_objects
colGaussianSmoothing.matrix	Non-documented_objects
colKernelSmoothing	colKernelSmoothing.matrix
colKernelSmoothing.matrix	colKernelSmoothing.matrix
colMeans	Non-documented_objects
colMeans.AromaTabularBinaryFile	Non-documented_objects
colMeans.default	Non-documented_objects
colorize	Non-documented_objects
colorize.Image	Non-documented_objects
colorize.RasterImage	Non-documented_objects
colStats	Non-documented_objects
colStats.AromaTabularBinaryFile	Non-documented_objects
colSums	Non-documented_objects
colSums.AromaTabularBinaryFile	Non-documented_objects
colSums.default	Non-documented_objects
convertTable	Non-documented_objects
convertTable.default	Non-documented_objects
CopyNumberChromosomalModel	CopyNumberChromosomalModel
CopyNumberChromosomalModel.estimateSds	estimateSds.CopyNumberChromosomalModel
CopyNumberChromosomalModel.extractRawCopyNumbers	extractRawCopyNumbers.CopyNumberChromosomalModel
CopyNumberChromosomalModel.fit	fit.CopyNumberChromosomalModel
CopyNumberDataFile	Non-documented_objects
CopyNumberDataSet	Non-documented_objects
CopyNumberDataSetTuple	Non-documented_objects
CopyNumberOutliers	Non-documented_objects
CopyNumberRegions	Non-documented_objects
CopyNumberSegmentationModel	CopyNumberSegmentationModel
CopyNumberSegmentationModel.fit	fit.CopyNumberSegmentationModel
countBases	Non-documented_objects
countBases.AromaCellSequenceFile	Non-documented_objects
countBasesInternal	Non-documented_objects
countBasesInternal.AromaCellSequenceFile	Non-documented_objects
createImage	Non-documented_objects
createImage.matrix	Non-documented_objects
DEFUNCT	Non-documented_objects
DEPRECATED	Non-documented_objects
dim.RichDataFrame	Non-documented_objects
dimnames<-.AromaTabularBinaryFile	Non-documented_objects
display	Non-documented_objects
display,Explorer-method	display.Explorer
display.ChromosomeExplorer	Non-documented_objects
display.Explorer	display.Explorer
display.Image	Non-documented_objects
display.RasterImage	Non-documented_objects
divideBy	Non-documented_objects
divideBy.RawGenomicSignals	Non-documented_objects
doCBS	doCBS
doCBS.character	doCBS
doCBS.CopyNumberDataSet	doCBS
doCBS.CopyNumberDataSetTuple	doCBS
doCBS.default	doCBS
downloadACC	Non-documented_objects
downloadACC.AromaRepository	Non-documented_objects
downloadACM	Non-documented_objects
downloadACM.AromaRepository	Non-documented_objects
downloadACP	Non-documented_objects
downloadACP.AromaRepository	Non-documented_objects
downloadACS	Non-documented_objects
downloadACS.AromaRepository	Non-documented_objects
downloadAll	Non-documented_objects
downloadAll.AromaRepository	Non-documented_objects
downloadCDF	Non-documented_objects
downloadCDF.AromaRepository	Non-documented_objects
downloadChipTypeFile	Non-documented_objects
downloadChipTypeFile,AromaRepository-method	downloadChipTypeFile.AromaRepository
downloadChipTypeFile.AromaRepository	downloadChipTypeFile.AromaRepository
downloadFile,AromaRepository-method	downloadFile.AromaRepository
downloadFile.AromaRepository	downloadFile.AromaRepository
downloadProbeSeqsTXT	Non-documented_objects
downloadProbeSeqsTXT.AromaRepository	Non-documented_objects
downloadTXT	Non-documented_objects
downloadTXT.AromaRepository	Non-documented_objects
downloadUFL	Non-documented_objects
downloadUFL.AromaRepository	Non-documented_objects
downloadUGC	Non-documented_objects
downloadUGC.AromaRepository	Non-documented_objects
downloadUGP	Non-documented_objects
downloadUGP.AromaRepository	Non-documented_objects
drawCnRegions	Non-documented_objects
drawCnRegions.DNAcopy	Non-documented_objects
drawCnRegions.HaarSeg	Non-documented_objects
drawCnRegions.MPCBS	Non-documented_objects
drawCnRegions.profileCGH	Non-documented_objects
drawCytoband	Non-documented_objects
drawCytoband.ChromosomalModel	Non-documented_objects
drawCytoband.profileCGH	Non-documented_objects
drawCytoband2	Non-documented_objects
drawCytoband2.default	Non-documented_objects
drawDensity	Non-documented_objects
drawDensity.CopyNumberRegions	Non-documented_objects
drawDensity.RawGenomicSignals	Non-documented_objects
drawExtraAnnotations	Non-documented_objects
drawExtraAnnotations.default	Non-documented_objects
drawExtraAnnotations.profileCGH	Non-documented_objects
drawLevels	Non-documented_objects
drawLevels.CopyNumberOutliers	Non-documented_objects
drawLevels.CopyNumberRegions	Non-documented_objects
dropAlpha	Non-documented_objects
dropAlpha.RasterImage	Non-documented_objects
dropRootPathTags.default	Non-documented_objects
dropSegmentationOutliers	Non-documented_objects
dropSegmentationOutliers.NonPairedPSCNData	Non-documented_objects
dropSegmentationOutliers.PairedPSCNData	Non-documented_objects
dropVirtualColumn	Non-documented_objects
dropVirtualColumn.RichDataFrame	Non-documented_objects
equals.AromaPlatform	Non-documented_objects
equals.CopyNumberRegions	Non-documented_objects
estimateSds	Non-documented_objects
estimateSds,CopyNumberChromosomalModel-method	estimateSds.CopyNumberChromosomalModel
estimateSds.CopyNumberChromosomalModel	estimateSds.CopyNumberChromosomalModel
estimateStandardDeviation	Non-documented_objects
estimateStandardDeviation,RawGenomicSignals-method	estimateStandardDeviation.RawGenomicSignals
estimateStandardDeviation.RawGenomicSignals	estimateStandardDeviation.RawGenomicSignals
Explorer	Explorer
Explorer.display	display.Explorer
Explorer.getAlias	getAlias.Explorer
Explorer.getName	getName.Explorer
Explorer.getNames	getNames.Explorer
Explorer.getPath	getPath.Explorer
Explorer.getRootPath	getRootPath.Explorer
Explorer.getTags	getTags.Explorer
Explorer.nbrOfArrays	nbrOfArrays.Explorer
Explorer.process	process.Explorer
Explorer.setAlias	setAlias.Explorer
Explorer.setArrays	setArrays.Explorer
exportAromaUnitPscnBinarySet	exportAromaUnitPscnBinarySet
exportAromaUnitPscnBinarySet.AromaUnitTotalCnBinarySet	exportAromaUnitPscnBinarySet
exportAromaUnitPscnBinarySet.list	exportAromaUnitPscnBinarySet
exportFracBDiffSet	Non-documented_objects
exportFracBDiffSet.AromaUnitFracBCnBinarySet	Non-documented_objects
exportTotalCnRatioSet	Non-documented_objects
exportTotalCnRatioSet.AromaUnitTotalCnBinarySet	Non-documented_objects
extractByChromosome	Non-documented_objects
extractByChromosome.AromaUnitChromosomeTabularBinaryFile	Non-documented_objects
extractByReferenceName	Non-documented_objects
extractByReferenceName.SegmentationDataSet	Non-documented_objects
extractBySampleName	Non-documented_objects
extractBySampleName.SegmentationDataSet	Non-documented_objects
extractCallArray	Non-documented_objects
extractCallArray.AromaUnitCallFile	Non-documented_objects
extractCallArray.AromaUnitCallSet	Non-documented_objects
extractCalls	Non-documented_objects
extractCalls.AromaUnitCallFile	Non-documented_objects
extractCalls.AromaUnitCallSet	Non-documented_objects
extractChromosome	Non-documented_objects
extractChromosome.RawGenomicSignals	Non-documented_objects
extractChromosomes	Non-documented_objects
extractChromosomes.RawGenomicSignals	Non-documented_objects
extractCNRs	Non-documented_objects
extractCNRs.default	Non-documented_objects
extractCopyNumberOutliers	Non-documented_objects
extractCopyNumberOutliers.DNAcopy	Non-documented_objects
extractCopyNumberOutliers.profileCGH	Non-documented_objects
extractCopyNumberRegions	Non-documented_objects
extractCopyNumberRegions.default	Non-documented_objects
extractCopyNumberRegions.DNAcopy	Non-documented_objects
extractCopyNumberRegions.HaarSeg	Non-documented_objects
extractCopyNumberRegions.MPCBS	Non-documented_objects
extractCopyNumberRegions.profileCGH	Non-documented_objects
extractCopyNumberRegions.SegmentationDataFile	Non-documented_objects
extractCopyNumberRegions.SegmentationDataSet	Non-documented_objects
extractDataForSegmentation	Non-documented_objects
extractDataForSegmentation.RawGenomicSignals	Non-documented_objects
extractGenotypeMatrix	Non-documented_objects
extractGenotypeMatrix.AromaUnitCallSet	Non-documented_objects
extractGenotypeMatrix.AromaUnitGenotypeCallFile	Non-documented_objects
extractGenotypes	Non-documented_objects
extractGenotypes.AromaUnitGenotypeCallFile	Non-documented_objects
extractGenotypes.AromaUnitGenotypeCallSet	Non-documented_objects
extractIGV	Non-documented_objects
extractIGV.CopyNumberRegions	Non-documented_objects
extractMatrix.AromaUnitCallFile	Non-documented_objects
extractMatrix.AromaUnitSignalBinaryFile	Non-documented_objects
extractMergedRawCopyNumbers	Non-documented_objects
extractMergedRawCopyNumbers.AromaUnitTotalCnBinaryFileList	Non-documented_objects
extractNonPairedPSCNData	Non-documented_objects
extractNonPairedPSCNData.PairedPSCNData	Non-documented_objects
extractOld	Non-documented_objects
extractOld.AromaMicroarrayDataSetTuple	Non-documented_objects
extractPSCNArray	Non-documented_objects
extractPSCNArray.AromaUnitTotalCnBinaryFile	Non-documented_objects
extractPSCNArray.AromaUnitTotalCnBinarySet	Non-documented_objects
extractPSCNMatrix	Non-documented_objects
extractPSCNMatrix.AromaUnitTotalCnBinaryFile	Non-documented_objects
extractRawAlleleBFractions	Non-documented_objects
extractRawAlleleBFractions.AromaUnitFracBCnBinaryFile	Non-documented_objects
extractRawAlleleBFractions.default	Non-documented_objects
extractRawCNs	Non-documented_objects
extractRawCNs.default	Non-documented_objects
extractRawCopyNumbers	Non-documented_objects
extractRawCopyNumbers,CopyNumberChromosomalModel-method	extractRawCopyNumbers.CopyNumberChromosomalModel
extractRawCopyNumbers.AromaUnitPscnBinaryFile	Non-documented_objects
extractRawCopyNumbers.AromaUnitTotalCnBinaryFile	Non-documented_objects
extractRawCopyNumbers.AromaUnitTotalCnBinaryFileList	Non-documented_objects
extractRawCopyNumbers.CopyNumberChromosomalModel	extractRawCopyNumbers.CopyNumberChromosomalModel
extractRawCopyNumbers.default	Non-documented_objects
extractRawCopyNumbers.DNAcopy	Non-documented_objects
extractRawCopyNumbers.HaarSeg	Non-documented_objects
extractRawCopyNumbers.profileCGH	Non-documented_objects
extractRawCopyNumbers.RawCopyNumbers	Non-documented_objects
extractRawCopyNumbers.RawSequenceReads	Non-documented_objects
extractRawGenomicSignals	Non-documented_objects
extractRawGenomicSignals.AromaUnitSignalBinaryFile	Non-documented_objects
extractRawGenomicSignals.AromaUnitTotalCnBinaryFileList	Non-documented_objects
extractRawGenomicSignals.default	Non-documented_objects
extractRawMirroredAlleleBFractions	Non-documented_objects
extractRawMirroredAlleleBFractions.default	Non-documented_objects
extractRawMirroredAlleleBFractions.RawAlleleBFractions	Non-documented_objects
extractRegion	Non-documented_objects
extractRegion.RawGenomicSignals	Non-documented_objects
extractRegions	Non-documented_objects
extractRegions.RawGenomicSignals	Non-documented_objects
extractSubset	Non-documented_objects
extractSubset.RawGenomicSignals	Non-documented_objects
extractSubsetByState	Non-documented_objects
extractSubsetByState.SegmentedGenomicSignalsInterface	Non-documented_objects
FileCacheKeyInterface	FileCacheKeyInterface
FileCacheKeyInterface.getCacheKey	getCacheKey.FileCacheKeyInterface
findAnnotationData	findAnnotationData
findAnnotationData.default	findAnnotationData
findAnnotationDataByChipType	findAnnotationDataByChipType
findAnnotationDataByChipType.AromaRepository	Non-documented_objects
findAnnotationDataByChipType.default	findAnnotationDataByChipType
findByChipType	Non-documented_objects
findByChipType.AromaMicroarrayTabularBinaryFile	Non-documented_objects
findByChipType.TextUnitNamesFile	Non-documented_objects
findByGenome	Non-documented_objects
findByGenome.AromaGenomeTextFile	Non-documented_objects
findByGenome.AromaUcscGenomeTextFile	Non-documented_objects
findByName.AromaUnitCallSet	Non-documented_objects
findByName.AromaUnitSignalBinarySet	Non-documented_objects
findChangePointsByState	Non-documented_objects
findChangePointsByState.SegmentedGenomicSignalsInterface	Non-documented_objects
findFilesTodo	Non-documented_objects
findFilesTodo,AromaTransform-method	findFilesTodo.AromaTransform
findFilesTodo.AromaTransform	findFilesTodo.AromaTransform
findLargeGaps	Non-documented_objects
findLargeGaps.AbstractCNData	Non-documented_objects
findPngDevice	Non-documented_objects
findPngDevice.default	Non-documented_objects
findSAFs	Non-documented_objects
findSAFs.SampleAnnotationSet	Non-documented_objects
findUnitNamesFile	Non-documented_objects
findUnitNamesFile.AromaPlatform	Non-documented_objects
findUnitsTodo	Non-documented_objects
findUnitsTodo.AromaUnitCallFile	Non-documented_objects
findUnitsTodo.AromaUnitCallSet	Non-documented_objects
findUnitTypesFile	Non-documented_objects
findUnitTypesFile.AromaPlatform	Non-documented_objects
fit	Non-documented_objects
fit,CopyNumberChromosomalModel-method	fit.CopyNumberChromosomalModel
fit,CopyNumberSegmentationModel-method	fit.CopyNumberSegmentationModel
fit.ChromosomalModel	Non-documented_objects
fit.CopyNumberChromosomalModel	fit.CopyNumberChromosomalModel
fit.CopyNumberSegmentationModel	fit.CopyNumberSegmentationModel
fit2d	Non-documented_objects
fit2d.matrix	Non-documented_objects
fitGenotypeCone	Non-documented_objects
fitGenotypeCone.matrix	fitGenotypeCone.matrix
fitGenotypeConeByExpectile	Non-documented_objects
fitGenotypeConeByExpectile.matrix	Non-documented_objects
fitGenotypeConeBySfit	Non-documented_objects
fitGenotypeConeBySfit.matrix	fitGenotypeConeBySfit.matrix
fitMultiDimensionalCone	Non-documented_objects
fitMultiDimensionalCone.matrix	fitMultiDimensionalCone.matrix
fitProbePositionEffects	Non-documented_objects
fitProbePositionEffects.numeric	Non-documented_objects
fitSplineBlockPolish	Non-documented_objects
fitSplineBlockPolish.matrix	Non-documented_objects
fitWHLAPLM	Non-documented_objects
fitWHLAPLM.matrix	Non-documented_objects
fitWHRCModel	Non-documented_objects
fitWHRCModel.matrix	Non-documented_objects
fitWLAPLM	Non-documented_objects
fitWLAPLM.matrix	Non-documented_objects
fitWRCModel	Non-documented_objects
fitWRCModel.matrix	Non-documented_objects
fitWRMA	Non-documented_objects
fitWRMA.matrix	Non-documented_objects
fixSearchPath	Non-documented_objects
fixSearchPath.AromaCore	Non-documented_objects
fixSearchPath.AromaPackage	Non-documented_objects
fixSearchPathInternal	Non-documented_objects
fixSearchPathInternal.AromaPackage	Non-documented_objects
fromFile.AromaUnitSignalBinaryFile	Non-documented_objects
fromPath	Non-documented_objects
fromPath.SampleAnnotationFile	Non-documented_objects
fromPath.SampleAnnotationSet	Non-documented_objects
gaussianSmoothing	Non-documented_objects
gaussianSmoothing.matrix	Non-documented_objects
gaussianSmoothing.numeric	Non-documented_objects
gaussianSmoothing.RawGenomicSignals	Non-documented_objects
gaussKernel	Non-documented_objects
getAlias	Non-documented_objects
getAlias,Explorer-method	getAlias.Explorer
getAlias.ChromosomalModel	Non-documented_objects
getAlias.Explorer	getAlias.Explorer
getAM	Non-documented_objects
getAM.AromaUnitTotalCnBinaryFile	Non-documented_objects
getAromaFullNameTranslatorSet	Non-documented_objects
getAromaFullNameTranslatorSet.AromaMicroarrayDataSet	Non-documented_objects
getAromaFullNameTranslatorSet.AromaUnitSignalBinarySet	Non-documented_objects
getAromaFullNameTranslatorSet.character	Non-documented_objects
getAromaGenomeTextFile	Non-documented_objects
getAromaGenomeTextFile.ChromosomalModel	Non-documented_objects
getAromaPlatform	Non-documented_objects
getAromaPlatform,AromaPlatformInterface-method	getAromaPlatform.AromaPlatformInterface
getAromaPlatform.AromaPlatformInterface	getAromaPlatform.AromaPlatformInterface
getAromaUflFile	Non-documented_objects
getAromaUflFile,AromaPlatformInterface-method	getUnitAnnotationDataFile.AromaPlatformInterface
getAromaUflFile.AromaPlatformInterface	getUnitAnnotationDataFile.AromaPlatformInterface
getAromaUflFile.UnitAnnotationDataFile	Non-documented_objects
getAromaUgpFile	Non-documented_objects
getAromaUgpFile,AromaPlatformInterface-method	getUnitAnnotationDataFile.AromaPlatformInterface
getAromaUgpFile.AromaPlatform	Non-documented_objects
getAromaUgpFile.AromaPlatformInterface	getUnitAnnotationDataFile.AromaPlatformInterface
getAromaUgpFile.AromaUnitSignalBinaryFile	Non-documented_objects
getAromaUgpFile.AromaUnitSignalBinarySet	Non-documented_objects
getAromaUgpFile.UnitAnnotationDataFile	Non-documented_objects
getArrays	Non-documented_objects
getArrays.AromaMicroarrayDataSetTuple	Non-documented_objects
getArrays.ChromosomalModel	Non-documented_objects
getArrays.Explorer	Non-documented_objects
getArraysOfInput	Non-documented_objects
getArraysOfInput.ChromosomeExplorer	Non-documented_objects
getArraysOfInput.Explorer	Non-documented_objects
getArrayTuple	Non-documented_objects
getArrayTuple.AromaMicroarrayDataSetTuple	Non-documented_objects
getAsteriskTags.AromaMicroarrayDataSetTuple	Non-documented_objects
getAsteriskTags.AromaTransform	Non-documented_objects
getAsteriskTags.ChromosomalModel	Non-documented_objects
getAsteriskTags.CopyNumberSegmentationModel	Non-documented_objects
getAsteriskTags.Explorer	Non-documented_objects
getAsteriskTags.HaarSegModel	Non-documented_objects
getAsteriskTags.RawCopyNumberModel	Non-documented_objects
getAttributeXY	Non-documented_objects
getAttributeXY.AromaMicroarrayDataFile	Non-documented_objects
getAverageFile	Non-documented_objects
getAverageFile.AromaMicroarrayDataSet	Non-documented_objects
getAverageFile.AromaUnitPscnBinarySet	Non-documented_objects
getAverageFile.AromaUnitTotalCnBinarySet	Non-documented_objects
getBasicField	Non-documented_objects
getBasicField.RawGenomicSignals	Non-documented_objects
getBytesPerColumn	Non-documented_objects
getBytesPerColumn.AromaTabularBinaryFile	Non-documented_objects
getCacheKey	Non-documented_objects
getCacheKey,CacheKeyInterface-method	getCacheKey.CacheKeyInterface
getCacheKey,FileCacheKeyInterface-method	getCacheKey.FileCacheKeyInterface
getCacheKey.CacheKeyInterface	getCacheKey.CacheKeyInterface
getCacheKey.FileCacheKeyInterface	getCacheKey.FileCacheKeyInterface
getChipEffectFiles	Non-documented_objects
getChipEffectFiles.ChromosomalModel	Non-documented_objects
getChipType	Non-documented_objects
getChipType,AromaPlatformInterface-method	getChipType.AromaPlatformInterface
getChipType,ChromosomalModel-method	getChipType.ChromosomalModel
getChipType.AbstractCNData	Non-documented_objects
getChipType.AromaMicroarrayDataFile	Non-documented_objects
getChipType.AromaMicroarrayDataSet	Non-documented_objects
getChipType.AromaMicroarrayTabularBinaryFile	Non-documented_objects
getChipType.AromaPlatformInterface	getChipType.AromaPlatformInterface
getChipType.AromaUnitSignalBinaryFile	Non-documented_objects
getChipType.AromaUnitSignalBinarySet	Non-documented_objects
getChipType.AromaUnitTypesFile	Non-documented_objects
getChipType.ChromosomalModel	getChipType.ChromosomalModel
getChipType.SegmentationDataSet	Non-documented_objects
getChipType.TextUnitNamesFile	Non-documented_objects
getChipType.UnitAnnotationDataFile	Non-documented_objects
getChipTypes	Non-documented_objects
getChipTypes.AromaMicroarrayDataSetTuple	Non-documented_objects
getChipTypes.ChromosomalModel	Non-documented_objects
getChromosome	Non-documented_objects
getChromosome.Arguments	Non-documented_objects
getChromosome.RawGenomicSignals	Non-documented_objects
getChromosome.SegmentationDataFile	Non-documented_objects
getChromosomeLabels	Non-documented_objects
getChromosomeLabels.ChromosomeExplorer	Non-documented_objects
getChromosomeLength	Non-documented_objects
getChromosomeLength.CopyNumberChromosomalModel	Non-documented_objects
getChromosomes	Non-documented_objects
getChromosomes,ChromosomalModel-method	getChromosomes.ChromosomalModel
getChromosomes,ChromosomeExplorer-method	getChromosomes.ChromosomeExplorer
getChromosomes.Arguments	Non-documented_objects
getChromosomes.AromaUnitChromosomeTabularBinaryFile	Non-documented_objects
getChromosomes.ChromosomalModel	getChromosomes.ChromosomalModel
getChromosomes.ChromosomeExplorer	getChromosomes.ChromosomeExplorer
getChromosomes.CopyNumberRegions	Non-documented_objects
getChromosomes.RawGenomicSignals	Non-documented_objects
getChromosomes.SegmentationDataSet	Non-documented_objects
getCn	Non-documented_objects
getCn.RawCopyNumbers	Non-documented_objects
getCNs	Non-documented_objects
getCNs.RawCopyNumbers	Non-documented_objects
getColClasses	Non-documented_objects
getColClasses.AromaTabularBinaryFile	Non-documented_objects
getColumnNames.AromaCellCpgFile	Non-documented_objects
getColumnNames.AromaCellPositionFile	Non-documented_objects
getColumnNames.AromaCellSequenceFile	Non-documented_objects
getColumnNames.AromaTabularBinaryFile	Non-documented_objects
getColumnNames.AromaUflFile	Non-documented_objects
getColumnNames.AromaUgpFile	Non-documented_objects
getColumnNames.AromaUnitChromosomeTabularBinaryFile	Non-documented_objects
getColumnNames.AromaUnitGcContentFile	Non-documented_objects
getColumnNames.AromaUnitPscnBinaryFile	Non-documented_objects
getColumnNames.RichDataFrame	Non-documented_objects
getColumnNamesTranslator	Non-documented_objects
getColumnNamesTranslator.RichDataFrame	Non-documented_objects
getCommonListElements	Non-documented_objects
getCXY	Non-documented_objects
getCXY.RawGenomicSignals	Non-documented_objects
getDataFileMatrix	Non-documented_objects
getDataFileMatrix.CopyNumberChromosomalModel	Non-documented_objects
getDefaultColumnNames.AromaCellCpgFile	Non-documented_objects
getDefaultColumnNames.AromaCellPositionFile	Non-documented_objects
getDefaultColumnNames.AromaCellSequenceFile	Non-documented_objects
getDefaultColumnNames.AromaTabularBinaryFile	Non-documented_objects
getDefaultColumnNames.AromaUflFile	Non-documented_objects
getDefaultColumnNames.AromaUgpFile	Non-documented_objects
getDefaultColumnNames.AromaUnitChromosomeTabularBinaryFile	Non-documented_objects
getDefaultColumnNames.AromaUnitGcContentFile	Non-documented_objects
getDefaultColumnNames.AromaUnitPscnBinaryFile	Non-documented_objects
getDefaultExtension	Non-documented_objects
getDefaultExtension.AromaCellCpgFile	Non-documented_objects
getDefaultExtension.AromaCellPositionFile	Non-documented_objects
getDefaultExtension.AromaCellSequenceFile	Non-documented_objects
getDefaultExtension.AromaUflFile	Non-documented_objects
getDefaultExtension.AromaUgpFile	Non-documented_objects
getDefaultExtension.UnitAnnotationDataFile	Non-documented_objects
getDefaultFullName.AromaMicroarrayDataSet	Non-documented_objects
getDefaultFullName.AromaTabularBinarySet	Non-documented_objects
getDefaultFullName.SegmentationDataSet	Non-documented_objects
getDefaultLocusFields	Non-documented_objects
getDefaultLocusFields.RawGenomicSignals	Non-documented_objects
getDensity	Non-documented_objects
getDensity.CopyNumberRegions	Non-documented_objects
getDeviceResolution	Non-documented_objects
getDeviceResolution.default	Non-documented_objects
getEffects	Non-documented_objects
getEffects.ProbePositionEffects	Non-documented_objects
getExpectedOutputFiles	Non-documented_objects
getExpectedOutputFiles.AromaTransform	Non-documented_objects
getExpectedOutputFullnames	Non-documented_objects
getExpectedOutputFullnames.AromaTransform	Non-documented_objects
getExtensionPattern.AromaCellPositionFile	Non-documented_objects
getExtensionPattern.AromaCellSequenceFile	Non-documented_objects
getExtensionPattern.AromaUflFile	Non-documented_objects
getExtensionPattern.AromaUgpFile	Non-documented_objects
getExtensionPattern.AromaUnitGcContentFile	Non-documented_objects
getExtensionPattern.AromaUnitSignalBinaryFile	Non-documented_objects
getExtensionPattern.SampleAnnotationFile	Non-documented_objects
getExtensionPattern.TextUnitNamesFile	Non-documented_objects
getFilenameExtension.AromaCellCpgFile	Non-documented_objects
getFilenameExtension.AromaCellPositionFile	Non-documented_objects
getFilenameExtension.AromaCellSequenceFile	Non-documented_objects
getFilenameExtension.AromaMicroarrayTabularBinaryFile	Non-documented_objects
getFilenameExtension.AromaUflFile	Non-documented_objects
getFilenameExtension.AromaUgpFile	Non-documented_objects
getFilenameExtension.AromaUnitChromosomeTabularBinaryFile	Non-documented_objects
getFilenameExtension.AromaUnitGcContentFile	Non-documented_objects
getFilenameExtension.AromaUnitSignalBinaryFile	Non-documented_objects
getFilenameExtension.TextUnitNamesFile	Non-documented_objects
getFitFunction	Non-documented_objects
getFitFunction.CbsModel	Non-documented_objects
getFitFunction.CopyNumberSegmentationModel	Non-documented_objects
getFitFunction.GladModel	Non-documented_objects
getFitFunction.HaarSegModel	Non-documented_objects
getFullName,AromaTransform-method	getFullName.AromaTransform
getFullName.AromaTransform	getFullName.AromaTransform
getFullName.ChromosomalModel	Non-documented_objects
getFullName.Explorer	Non-documented_objects
getFullName.RichDataFrame	Non-documented_objects
getFullNames.AromaMicroarrayDataSetTuple	Non-documented_objects
getFullNames.ChromosomalModel	Non-documented_objects
getFullNames.ChromosomeExplorer	Non-documented_objects
getFullNames.CopyNumberSegmentationModel	Non-documented_objects
getFullNameTranslatorSet	Non-documented_objects
getFullNameTranslatorSet.character	Non-documented_objects
getFullNameTranslatorSet.GenericDataFileSet	Non-documented_objects
getGenericSummary	Non-documented_objects
getGenericSummary.RichDataFrame	Non-documented_objects
getGenome	Non-documented_objects
getGenome.ChromosomalModel	Non-documented_objects
getGenomeData	Non-documented_objects
getGenomeData.ChromosomalModel	Non-documented_objects
getGenomeFile	Non-documented_objects
getGenomeFile.ChromosomalModel	Non-documented_objects
getGenomeVersion	Non-documented_objects
getGenomeVersion.AromaUnitChromosomeTabularBinaryFile	Non-documented_objects
getHeaderParameters	Non-documented_objects
getHeaderParameters.TextUnitNamesFile	Non-documented_objects
getImage	Non-documented_objects
getImage.matrix	Non-documented_objects
getImageData	Non-documented_objects
getImageData.Image	Non-documented_objects
getImageData.RasterImage	Non-documented_objects
getIncludePath	Non-documented_objects
getIncludePath.Explorer	Non-documented_objects
getInputDataSet	Non-documented_objects
getInputDataSet,AromaTransform-method	getInputDataSet.AromaTransform
getInputDataSet.AromaTransform	getInputDataSet.AromaTransform
getLength	Non-documented_objects
getLength.CopyNumberRegions	Non-documented_objects
getListOfAromaUgpFiles	Non-documented_objects
getListOfAromaUgpFiles.ChromosomalModel	Non-documented_objects
getListOfChipEffectSets	Non-documented_objects
getListOfChipEffectSets.ChromosomalModel	Non-documented_objects
getListOfUnitNamesFiles	Non-documented_objects
getListOfUnitNamesFiles.AromaUnitTotalCnBinarySetTuple	Non-documented_objects
getListOfUnitNamesFiles.ChromosomalModel	Non-documented_objects
getListOfUnitTypesFiles	Non-documented_objects
getListOfUnitTypesFiles.ChromosomalModel	Non-documented_objects
getLociFields	Non-documented_objects
getLociFields.RawGenomicSignals	Non-documented_objects
getLocusData	Non-documented_objects
getLocusData.AbstractCNData	Non-documented_objects
getLocusFields	Non-documented_objects
getLocusFields.RawGenomicSignals	Non-documented_objects
getLog2Ratios	Non-documented_objects
getLog2Ratios.CopyNumberSegmentationModel	Non-documented_objects
getMainPath	Non-documented_objects
getMainPath.Explorer	Non-documented_objects
getMaxLengthRepeats	Non-documented_objects
getMaxLengthRepeats.AromaCellSequenceFile	Non-documented_objects
getMaxNAFraction	Non-documented_objects
getMaxNAFraction.CopyNumberChromosomalModel	Non-documented_objects
getMeanAt	Non-documented_objects
getMeanAt.CopyNumberRegions	Non-documented_objects
getModel	Non-documented_objects
getModel,ChromosomeExplorer-method	getModel.ChromosomeExplorer
getModel.ChromosomeExplorer	getModel.ChromosomeExplorer
getName,AromaTransform-method	getName.AromaTransform
getName,Explorer-method	getName.Explorer
getName.AromaPlatform	Non-documented_objects
getName.AromaTransform	getName.AromaTransform
getName.ChromosomalModel	Non-documented_objects
getName.Explorer	getName.Explorer
getName.RawGenomicSignals	Non-documented_objects
getName.RichDataFrame	Non-documented_objects
getNameOfInput	Non-documented_objects
getNameOfInput.ChromosomeExplorer	Non-documented_objects
getNameOfInput.Explorer	Non-documented_objects
getNames,ChromosomalModel-method	getNames.ChromosomalModel
getNames,Explorer-method	getNames.Explorer
getNames.ChromosomalModel	getNames.ChromosomalModel
getNames.ChromosomeExplorer	Non-documented_objects
getNames.CopyNumberChromosomalModel	Non-documented_objects
getNames.Explorer	getNames.Explorer
getNumberOfFilesAveraged	Non-documented_objects
getNumberOfFilesAveraged.AromaUnitSignalBinaryFile	Non-documented_objects
getNumberOfFilesAveraged.CopyNumberDataFile	Non-documented_objects
getOption	Non-documented_objects
getOptionalArguments	Non-documented_objects
getOptionalArguments.CopyNumberChromosomalModel	Non-documented_objects
getOutputDataSet	Non-documented_objects
getOutputDataSet,AromaTransform-method	getOutputDataSet.AromaTransform
getOutputDataSet.AromaTransform	getOutputDataSet.AromaTransform
getOutputDataSet0	Non-documented_objects
getOutputDataSet0.AromaTransform	Non-documented_objects
getOutputFiles	Non-documented_objects
getOutputFiles.AromaTransform	Non-documented_objects
getOutputSet	Non-documented_objects
getOutputSet.ChromosomalModel	Non-documented_objects
getPairedNames	Non-documented_objects
getPairedNames.CopyNumberChromosomalModel	Non-documented_objects
getParallelSafe	Non-documented_objects
getParallelSafe.Explorer	Non-documented_objects
getParameters	Non-documented_objects
getParameters,ParametersInterface-method	getParameters.ParametersInterface
getParameters.ParametersInterface	getParameters.ParametersInterface
getParametersAsString	Non-documented_objects
getParametersAsString,ParametersInterface-method	getParametersAsString.ParametersInterface
getParametersAsString.ParametersInterface	getParametersAsString.ParametersInterface
getParameterSets	Non-documented_objects
getParameterSets.ParametersInterface	Non-documented_objects
getParentName	Non-documented_objects
getParentName.GenericDataFile	Non-documented_objects
getParentName.GenericDataFileSet	Non-documented_objects
getParentPath	Non-documented_objects
getParentPath.ChromosomalModel	Non-documented_objects
getPath,AromaTransform-method	getPath.AromaTransform
getPath,Explorer-method	getPath.Explorer
getPath.AromaTransform	getPath.AromaTransform
getPath.ChromosomalModel	Non-documented_objects
getPath.ChromosomeExplorer	Non-documented_objects
getPath.Explorer	getPath.Explorer
getPatterns	Non-documented_objects
getPatterns.SampleAnnotationFile	Non-documented_objects
getPhysicalPositions	Non-documented_objects
getPhysicalPositions.RawCopyNumbers	Non-documented_objects
getPlatform	Non-documented_objects
getPlatform,AromaPlatformInterface-method	getPlatform.AromaPlatformInterface
getPlatform.AbstractCNData	Non-documented_objects
getPlatform.AromaMicroarrayDataFile	Non-documented_objects
getPlatform.AromaMicroarrayDataSet	Non-documented_objects
getPlatform.AromaMicroarrayTabularBinaryFile	Non-documented_objects
getPlatform.AromaPlatformInterface	getPlatform.AromaPlatformInterface
getPlatform.AromaUnitSignalBinaryFile	Non-documented_objects
getPlatform.AromaUnitSignalBinarySet	Non-documented_objects
getPlatform.AromaUnitTypesFile	Non-documented_objects
getPlatform.TextUnitNamesFile	Non-documented_objects
getPlatform.UnitAnnotationDataFile	Non-documented_objects
getPloidy	Non-documented_objects
getPloidy.AromaMicroarrayDataFile	Non-documented_objects
getPositions	Non-documented_objects
getPositions.AromaUgpFile	Non-documented_objects
getPositions.RawGenomicSignals	Non-documented_objects
getProbeLength	Non-documented_objects
getProbeLength.AromaCellSequenceFile	Non-documented_objects
getProbePositionEffectDesignMatrix	Non-documented_objects
getProbePositionEffectDesignMatrix.character	Non-documented_objects
getProbePositionEffectDesignMatrix.raw	Non-documented_objects
getRam	Non-documented_objects
getRam.AromaSettings	Non-documented_objects
getRandomSeed	Non-documented_objects
getRandomSeed.CbsModel	Non-documented_objects
getRawCnData	Non-documented_objects
getRawCnData.CopyNumberChromosomalModel	Non-documented_objects
getReference	Non-documented_objects
getReference.CopyNumberChromosomalModel	Non-documented_objects
getReferenceName	Non-documented_objects
getReferenceName.SegmentationDataFile	Non-documented_objects
getReferenceNames	Non-documented_objects
getReferenceNames.SegmentationDataSet	Non-documented_objects
getReferenceSetTuple	Non-documented_objects
getReferenceSetTuple.CopyNumberChromosomalModel	Non-documented_objects
getRefSetTuple	Non-documented_objects
getRefSetTuple.CopyNumberChromosomalModel	Non-documented_objects
getRegions	Non-documented_objects
getRegions.CopyNumberSegmentationModel	Non-documented_objects
getReportPath	Non-documented_objects
getReportPath.ChromosomalModel	Non-documented_objects
getReportPathPattern	Non-documented_objects
getReportPathPattern.Explorer	Non-documented_objects
getRootName	Non-documented_objects
getRootName.AromaTabularBinaryFile	Non-documented_objects
getRootName.AromaTabularBinarySet	Non-documented_objects
getRootPath	Non-documented_objects
getRootPath,AromaTransform-method	getRootPath.AromaTransform
getRootPath,Explorer-method	getRootPath.Explorer
getRootPath.AromaTransform	getRootPath.AromaTransform
getRootPath.ChromosomalModel	Non-documented_objects
getRootPath.Explorer	getRootPath.Explorer
getSampleLabels	Non-documented_objects
getSampleLabels.ChromosomeExplorer	Non-documented_objects
getSampleLayerName	Non-documented_objects
getSampleLayerName.Explorer	Non-documented_objects
getSampleLayerPrefix	Non-documented_objects
getSampleLayerPrefix.Explorer	Non-documented_objects
getSampleName	Non-documented_objects
getSampleName.SegmentationDataFile	Non-documented_objects
getSampleNames	Non-documented_objects
getSampleNames.SegmentationDataSet	Non-documented_objects
getSets.AromaMicroarrayDataSetTuple	Non-documented_objects
getSets.ChromosomalModel	Non-documented_objects
getSetTag	Non-documented_objects
getSetTag.ChromosomalModel	Non-documented_objects
getSetTag.RawCopyNumberModel	Non-documented_objects
getSetTuple	Non-documented_objects
getSetTuple.ChromosomalModel	Non-documented_objects
getSigma	Non-documented_objects
getSigma.RawGenomicSignals	Non-documented_objects
getSignalColumnName	Non-documented_objects
getSignalColumnName.RawGenomicSignals	Non-documented_objects
getSignalColumnNames	Non-documented_objects
getSignalColumnNames.NonPairedPSCNData	Non-documented_objects
getSignalColumnNames.PairedPSCNData	Non-documented_objects
getSignalColumnNames.RawGenomicSignals	Non-documented_objects
getSignals	Non-documented_objects
getSignals.RawCopyNumbers	Non-documented_objects
getSignals.RawGenomicSignals	Non-documented_objects
getSNPFields	Non-documented_objects
getSNPFields.AbstractPSCNData	Non-documented_objects
getSnpNucleotides	Non-documented_objects
getSnpNucleotides.AromaCellSequenceFile	Non-documented_objects
getSnpPositions	Non-documented_objects
getSnpPositions.AromaCellSequenceFile	Non-documented_objects
getSnpShifts	Non-documented_objects
getSnpShifts.AromaCellSequenceFile	Non-documented_objects
getStateColorMap	Non-documented_objects
getStateColorMap.SegmentedGenomicSignalsInterface	Non-documented_objects
getStateColors	Non-documented_objects
getStateColors.SegmentedGenomicSignalsInterface	Non-documented_objects
getStates	Non-documented_objects
getStates.SegmentedGenomicSignalsInterface	Non-documented_objects
getSubname	Non-documented_objects
getSubname.Explorer	Non-documented_objects
getTableOfArrays	Non-documented_objects
getTableOfArrays.AromaMicroarrayDataSetTuple	Non-documented_objects
getTableOfArrays.ChromosomalModel	Non-documented_objects
getTags,AromaTransform-method	getTags.AromaTransform
getTags,Explorer-method	getTags.Explorer
getTags.Arguments	Non-documented_objects
getTags.AromaMicroarrayDataSetTuple	Non-documented_objects
getTags.AromaTransform	getTags.AromaTransform
getTags.ChromosomalModel	Non-documented_objects
getTags.CopyNumberSegmentationModel	Non-documented_objects
getTags.Explorer	getTags.Explorer
getTags.RichDataFrame	Non-documented_objects
getTagsOfInput	Non-documented_objects
getTagsOfInput.ChromosomeExplorer	Non-documented_objects
getTagsOfInput.Explorer	Non-documented_objects
getTCNs	Non-documented_objects
getTCNs.PairedPSCNData	Non-documented_objects
getTemplatePath	Non-documented_objects
getTemplatePath.Explorer	Non-documented_objects
getTotalCopyNumbers	Non-documented_objects
getTotalCopyNumbers.PairedPSCNData	Non-documented_objects
getUniqueStates	Non-documented_objects
getUniqueStates.SegmentedGenomicSignalsInterface	Non-documented_objects
getUnitAnnotationDataFile	Non-documented_objects
getUnitAnnotationDataFile,AromaPlatformInterface-method	getUnitAnnotationDataFile.AromaPlatformInterface
getUnitAnnotationDataFile.AromaPlatformInterface	getUnitAnnotationDataFile.AromaPlatformInterface
getUnitNames	Non-documented_objects
getUnitNames.TextUnitNamesFile	Non-documented_objects
getUnitNames.UnitNamesFile	Non-documented_objects
getUnitNamesFile	Non-documented_objects
getUnitNamesFile,AromaPlatformInterface-method	getUnitAnnotationDataFile.AromaPlatformInterface
getUnitNamesFile.AromaPlatform	Non-documented_objects
getUnitNamesFile.AromaPlatformInterface	getUnitAnnotationDataFile.AromaPlatformInterface
getUnitNamesFile.AromaUnitTotalCnBinarySet	Non-documented_objects
getUnitsAt	Non-documented_objects
getUnitsAt.AromaUgpFile	Non-documented_objects
getUnitsOnChromosome	Non-documented_objects
getUnitsOnChromosome.AromaUgpFile	Non-documented_objects
getUnitsOnChromosome.AromaUnitChromosomeTabularBinaryFile	Non-documented_objects
getUnitsOnChromosomes	Non-documented_objects
getUnitsOnChromosomes.AromaUnitChromosomeTabularBinaryFile	Non-documented_objects
getUnitTypes	Non-documented_objects
getUnitTypes.AromaUnitTypesFile	Non-documented_objects
getUnitTypes.UnitTypesFile	Non-documented_objects
getUnitTypesFile	Non-documented_objects
getUnitTypesFile,AromaPlatformInterface-method	getUnitAnnotationDataFile.AromaPlatformInterface
getUnitTypesFile.AromaPlatform	Non-documented_objects
getUnitTypesFile.AromaPlatformInterface	getUnitAnnotationDataFile.AromaPlatformInterface
getUrlPath	Non-documented_objects
getUrlPath.AromaRepository	Non-documented_objects
getValueAt	Non-documented_objects
getValueAt.CopyNumberRegions	Non-documented_objects
getVerbose.AromaRepository	Non-documented_objects
getVerbose.AromaSettings	Non-documented_objects
getVersion.Explorer	Non-documented_objects
getVirtualColumn	Non-documented_objects
getVirtualColumn.RichDataFrame	Non-documented_objects
getVirtualColumnFunction	Non-documented_objects
getVirtualColumnFunction.RichDataFrame	Non-documented_objects
getVirtualColumnFunctions	Non-documented_objects
getVirtualColumnFunctions.RichDataFrame	Non-documented_objects
getVirtualColumnNames	Non-documented_objects
getVirtualColumnNames.RichDataFrame	Non-documented_objects
getVirtualField	Non-documented_objects
getVirtualField.SegmentedGenomicSignalsInterface	Non-documented_objects
getVirtualLocusFields	Non-documented_objects
getVirtualLocusFields.RawGenomicSignals	Non-documented_objects
getVirtualLocusFields.SegmentedGenomicSignalsInterface	Non-documented_objects
getWeights	Non-documented_objects
getWeights.RawGenomicSignals	Non-documented_objects
getXAM	Non-documented_objects
getXAM.AromaMicroarrayDataFile	Non-documented_objects
getXAM.AromaUnitTotalCnBinaryFile	Non-documented_objects
getXScale	Non-documented_objects
getXScale.RawGenomicSignals	Non-documented_objects
getXY	Non-documented_objects
getXY.RawGenomicSignals	Non-documented_objects
getYScale	Non-documented_objects
getYScale.RawGenomicSignals	Non-documented_objects
getZooms	Non-documented_objects
getZooms.ChromosomeExplorer	Non-documented_objects
GladModel	GladModel
groupBySnpNucleotides	Non-documented_objects
groupBySnpNucleotides.AromaCellSequenceFile	Non-documented_objects
HaarSegModel	HaarSegModel
hasAlleleBFractions	Non-documented_objects
hasAlleleBFractions.AromaUnitPscnBinaryFile	Non-documented_objects
hasAlleleBFractions.AromaUnitTotalCnBinaryFile	Non-documented_objects
hasAlleleBFractions.CopyNumberDataFile	Non-documented_objects
hasAlleleBFractions.CopyNumberDataSet	Non-documented_objects
hasAlleleBFractions.CopyNumberDataSetTuple	Non-documented_objects
hasAttributeXY	Non-documented_objects
hasAttributeXY.AromaMicroarrayDataFile	Non-documented_objects
hasColumn	Non-documented_objects
hasColumn.RichDataFrame	Non-documented_objects
hasColumns	Non-documented_objects
hasColumns.RichDataFrame	Non-documented_objects
hasKnownPositions	Non-documented_objects
hasKnownPositions.AbstractCNData	Non-documented_objects
hasStrandiness	Non-documented_objects
hasStrandiness.AromaUnitPscnBinaryFile	Non-documented_objects
hasStrandiness.AromaUnitTotalCnBinaryFile	Non-documented_objects
hasStrandiness.CopyNumberDataFile	Non-documented_objects
hasStrandiness.CopyNumberDataSet	Non-documented_objects
hasStrandiness.CopyNumberDataSetTuple	Non-documented_objects
hasTotalCopyNumberRatios	Non-documented_objects
hasTotalCopyNumberRatios.AromaUnitPscnBinaryFile	Non-documented_objects
hasVirtualColumn	Non-documented_objects
hasVirtualColumn.RichDataFrame	Non-documented_objects
hasVirtualColumns	Non-documented_objects
hasVirtualColumns.RichDataFrame	Non-documented_objects
hasWeights	Non-documented_objects
hasWeights.RawGenomicSignals	Non-documented_objects
importFrom	Non-documented_objects
importFrom.AromaTabularBinaryFile	Non-documented_objects
importFromGenericTabularFile	Non-documented_objects
importFromGenericTabularFile.AromaUflFile	Non-documented_objects
importFromGenericTabularFile.AromaUgpFile	Non-documented_objects
importFromTable	Non-documented_objects
importFromTable.FileMatrix	Non-documented_objects
importFromUnitTypesFile	Non-documented_objects
importFromUnitTypesFile.AromaUnitTypesFile	Non-documented_objects
indexOf,UnitNamesFile-method	indexOf.UnitNamesFile
indexOf.AromaMicroarrayDataSetTuple	Non-documented_objects
indexOf.ChromosomalModel	Non-documented_objects
indexOf.ChromosomeExplorer	Non-documented_objects
indexOf.UnitNamesFile	indexOf.UnitNamesFile
indexOfColumn	Non-documented_objects
indexOfColumn.AromaUnitChromosomeTabularBinaryFile	Non-documented_objects
indexOfUnits	Non-documented_objects
indexOfUnits.AromaUnitTabularBinaryFile	Non-documented_objects
interleave	Non-documented_objects
interleave.Image	Non-documented_objects
interleave.RasterImage	Non-documented_objects
isAverageFile	Non-documented_objects
isAverageFile.AromaMicroarrayDataFile	Non-documented_objects
isAverageFile.AromaUnitSignalBinaryFile	Non-documented_objects
isCompatibleWith	Non-documented_objects
isCompatibleWith,AromaPlatformInterface-method	isCompatibleWith.AromaPlatformInterface
isCompatibleWith.AromaPlatformInterface	isCompatibleWith.AromaPlatformInterface
isDone,AromaTransform-method	isDone.AromaTransform
isDone.AromaTransform	isDone.AromaTransform
isHeterozygote	Non-documented_objects
isHeterozygote.AromaUnitGenotypeCallFile	Non-documented_objects
isHeterozygous	Non-documented_objects
isHeterozygous.AromaUnitGenotypeCallFile	Non-documented_objects
isHomozygote	Non-documented_objects
isHomozygote.AromaUnitGenotypeCallFile	Non-documented_objects
isHomozygous	Non-documented_objects
isHomozygous.AromaUnitGenotypeCallFile	Non-documented_objects
isMissing	Non-documented_objects
isMissing.AromaCellCpgFile	Non-documented_objects
isMissing.AromaCellPositionFile	Non-documented_objects
isMissing.AromaCellSequenceFile	Non-documented_objects
isPaired	Non-documented_objects
isPaired.CopyNumberChromosomalModel	Non-documented_objects
kernelSmoothing	colKernelSmoothing.matrix
kernelSmoothing.numeric	colKernelSmoothing.matrix
kernelSmoothing.RawGenomicSignals	Non-documented_objects
kernelSmoothingByState	Non-documented_objects
kernelSmoothingByState.SegmentedGenomicSignalsInterface	Non-documented_objects
lapply	Non-documented_objects
lapplyInChunks	Non-documented_objects
lapplyInChunks.numeric	Non-documented_objects
length.RichDataFrame	Non-documented_objects
library	Non-documented_objects
lines.CopyNumberOutliers	Non-documented_objects
lines.CopyNumberRegions	Non-documented_objects
lines.RawGenomicSignals	Non-documented_objects
listFiles	Non-documented_objects
listFiles,AromaRepository-method	listFiles.AromaRepository
listFiles.AromaRepository	listFiles.AromaRepository
listToXml	Non-documented_objects
listToXml.list	Non-documented_objects
loadAll	Non-documented_objects
loadAll.SampleAnnotationSet	Non-documented_objects
loadFit	Non-documented_objects
loadFit.CbsSegmentationDataFile	Non-documented_objects
loadFit.SegmentationDataFile	Non-documented_objects
locallyUnique	Non-documented_objects
locallyUnique.default	Non-documented_objects
log2abs	Non-documented_objects
log2center	Non-documented_objects
log2neg	Non-documented_objects
log2pos	Non-documented_objects
matchPatterns	Non-documented_objects
matchPatterns.SampleAnnotationFile	Non-documented_objects
matrixBlockPolish	Non-documented_objects
matrixBlockPolish.matrix	matrixBlockPolish.matrix
mergeBoxplotStats	Non-documented_objects
mergeBoxplotStats.list	mergeBoxplotStats.list
MISC.	Non-documented_objects
multiplyBy	Non-documented_objects
multiplyBy.RawGenomicSignals	Non-documented_objects
names.RichDataFrame	Non-documented_objects
nbrOfArrays	Non-documented_objects
nbrOfArrays,ChromosomalModel-method	nbrOfArrays.ChromosomalModel
nbrOfArrays,Explorer-method	nbrOfArrays.Explorer
nbrOfArrays.ChromosomalModel	nbrOfArrays.ChromosomalModel
nbrOfArrays.Explorer	nbrOfArrays.Explorer
nbrOfCells	Non-documented_objects
nbrOfCells.AromaCellTabularBinaryFile	Non-documented_objects
nbrOfChipTypes	Non-documented_objects
nbrOfChipTypes,AromaMicroarrayDataSetTuple-method	nbrOfChipTypes.AromaMicroarrayDataSetTuple
nbrOfChipTypes,ChromosomalModel-method	nbrOfChipTypes.ChromosomalModel
nbrOfChipTypes.AromaMicroarrayDataSetTuple	nbrOfChipTypes.AromaMicroarrayDataSetTuple
nbrOfChipTypes.ChromosomalModel	nbrOfChipTypes.ChromosomalModel
nbrOfChromosomes	Non-documented_objects
nbrOfChromosomes.CopyNumberRegions	Non-documented_objects
nbrOfChromosomes.RawGenomicSignals	Non-documented_objects
nbrOfColumns.AromaTabularBinaryFile	Non-documented_objects
nbrOfEnzymes	Non-documented_objects
nbrOfEnzymes.AromaUflFile	Non-documented_objects
nbrOfLoci	Non-documented_objects
nbrOfLoci.RawGenomicSignals	Non-documented_objects
nbrOfReads	Non-documented_objects
nbrOfReads.RawSequenceReads	Non-documented_objects
nbrOfRegions	Non-documented_objects
nbrOfRegions.CopyNumberOutliers	Non-documented_objects
nbrOfRegions.CopyNumberRegions	Non-documented_objects
nbrOfRows.AromaTabularBinaryFile	Non-documented_objects
nbrOfUnits	Non-documented_objects
nbrOfUnits.AromaUnitSignalBinaryFile	Non-documented_objects
nbrOfUnits.AromaUnitTabularBinaryFile	Non-documented_objects
nbrOfUnits.TextUnitNamesFile	Non-documented_objects
nbrOfUnits.UnitAnnotationDataFile	Non-documented_objects
nbrOfUnits.UnitNamesFile	Non-documented_objects
nbrOfUnits.UnitTypesFile	Non-documented_objects
newInstance.RawGenomicSignals	Non-documented_objects
newInstance.RichDataFrame	Non-documented_objects
newPlot	Non-documented_objects
newPlot.CopyNumberChromosomalModel	Non-documented_objects
Non-documented objects	Non-documented_objects
NonPairedPSCNData	NonPairedPSCNData
norm2d	Non-documented_objects
norm2d.matrix	Non-documented_objects
normalizeGenotypeCone	Non-documented_objects
normalizeGenotypeCone.matrix	Non-documented_objects
normalizeTumorBoost	Non-documented_objects
normalizeTumorBoost.PairedPSCNData	Non-documented_objects
onFitAddGenotypeCalls	Non-documented_objects
onFitAddGenotypeCalls.default	Non-documented_objects
onFitAddGenotypeCalls.GladModel	Non-documented_objects
orderAlongGenome	Non-documented_objects
orderAlongGenome.AbstractCNData	Non-documented_objects
PairedPSCNData	PairedPSCNData
PairedPSCNData.plotTracks	plotTracks.PairedPSCNData
ParametersInterface	ParametersInterface
ParametersInterface.getParameters	getParameters.ParametersInterface
ParametersInterface.getParametersAsString	getParametersAsString.ParametersInterface
plot.BinnedScatter	Non-documented_objects
plot.CopyNumberSegmentationModel	Non-documented_objects
plot.ProbePositionEffects	Non-documented_objects
plot.RawAlleleBFractions	Non-documented_objects
plot.RawCopyNumbers	Non-documented_objects
plot.RawGenomicSignals	Non-documented_objects
plot.RawMirroredAlleleBFractions	Non-documented_objects
plot.RawSequenceReads	Non-documented_objects
plot.SegmentedGenomicSignalsInterface	Non-documented_objects
plotAxesLayers	Non-documented_objects
plotAxesLayers.CopyNumberChromosomalModel	Non-documented_objects
plotChromosomesLayers	Non-documented_objects
plotChromosomesLayers.CopyNumberChromosomalModel	Non-documented_objects
plotCopyNumberRegionLayers	Non-documented_objects
plotCopyNumberRegionLayers.CopyNumberSegmentationModel	Non-documented_objects
plotCoverageMap	Non-documented_objects
plotCoverageMap.AromaUgpFile	Non-documented_objects
plotCytobandLayers	Non-documented_objects
plotCytobandLayers.CopyNumberChromosomalModel	Non-documented_objects
plotFitLayers	Non-documented_objects
plotFitLayers.CopyNumberChromosomalModel	Non-documented_objects
plotGridHorizontalLayers	Non-documented_objects
plotGridHorizontalLayers.CopyNumberChromosomalModel	Non-documented_objects
plotProfile2	Non-documented_objects
plotProfile2.profileCGH	Non-documented_objects
plotRawCNs	Non-documented_objects
plotRawCNs.profileCGH	Non-documented_objects
plotRawCopyNumbers	Non-documented_objects
plotRawCopyNumbers.CopyNumberChromosomalModel	Non-documented_objects
plotSampleLayers	Non-documented_objects
plotSampleLayers.CopyNumberChromosomalModel	Non-documented_objects
plotTracks	plotTracks.PairedPSCNData
plotTracks,PairedPSCNData-method	plotTracks.PairedPSCNData
plotTracks.PairedPSCNData	plotTracks.PairedPSCNData
points.BinnedScatter	Non-documented_objects
points.RawGenomicSignals	Non-documented_objects
points.SegmentedGenomicSignalsInterface	Non-documented_objects
pointsRawCNs	Non-documented_objects
pointsRawCNs.default	Non-documented_objects
pointsRawCNs.profileCGH	Non-documented_objects
pointsSequence	Non-documented_objects
pointsSequence.ProbePositionEffects	Non-documented_objects
predict.ProbePositionEffects	Non-documented_objects
print.RawGenomicSignals	Non-documented_objects
print.RichDataFrame	Non-documented_objects
process	Non-documented_objects
process,AromaTransform-method	process.AromaTransform
process,ChromosomeExplorer-method	process.ChromosomeExplorer
process,Explorer-method	process.Explorer
process.AromaTransform	process.AromaTransform
process.ChromosomeExplorer	process.ChromosomeExplorer
process.Explorer	process.Explorer
processTime	processTime
processTime.default	processTime
prune	Non-documented_objects
prune.CopyNumberRegions	Non-documented_objects
RasterImage	Non-documented_objects
RawAlleleBFractions	RawAlleleBFractions
RawCopyNumberModel	RawCopyNumberModel
RawCopyNumbers	RawCopyNumbers
RawGenomicSignals	RawGenomicSignals
RawGenomicSignals.estimateStandardDeviation	estimateStandardDeviation.RawGenomicSignals
RawGenomicSignals.segmentByCBS	segmentByCBS.RawGenomicSignals
RawGenomicSignals.segmentByGLAD	segmentByGLAD.RawGenomicSignals
RawGenomicSignals.segmentByHaarSeg	segmentByHaarSeg.RawGenomicSignals
RawGenomicSignals.segmentByMPCBS	segmentByMPCBS.RawGenomicSignals
RawMirroredAlleleBFractions	RawMirroredAlleleBFractions
RawSequenceReads	RawSequenceReads
rbind.RichDataFrame	Non-documented_objects
read	Non-documented_objects
read.RasterImage	Non-documented_objects
readColumns.AromaTabularBinaryFile	Non-documented_objects
readCpgs	Non-documented_objects
readCpgs.AromaCellCpgFile	Non-documented_objects
readDataFrame.AromaGenomeTextFile	Non-documented_objects
readDataFrame.AromaTabularBinaryFile	Non-documented_objects
readDataFrame.AromaUcscGenomeTextFile	Non-documented_objects
readDataFrame.AromaUflFile	Non-documented_objects
readDataFrame.AromaUnitChromosomeTabularBinaryFile	Non-documented_objects
readDataFrame.AromaUnitSignalBinaryFile	Non-documented_objects
readDataFrame.SampleAnnotationFile	Non-documented_objects
readFooter	Non-documented_objects
readFooter,AromaTabularBinaryFile-method	readFooter.AromaTabularBinaryFile
readFooter.AromaTabularBinaryFile	readFooter.AromaTabularBinaryFile
readHeader	Non-documented_objects
readHeader.AromaTabularBinaryFile	Non-documented_objects
readNeighborSequenceMatrix	Non-documented_objects
readNeighborSequenceMatrix.AromaCellSequenceFile	Non-documented_objects
readPairSequenceMatrix	Non-documented_objects
readPairSequenceMatrix.AromaCellSequenceFile	Non-documented_objects
readPositions	Non-documented_objects
readPositions.AromaCellPositionFile	Non-documented_objects
readRawFooter	Non-documented_objects
readRawFooter.AromaTabularBinaryFile	Non-documented_objects
readSequenceMatrix	Non-documented_objects
readSequenceMatrix.AromaCellSequenceFile	Non-documented_objects
readSequences	Non-documented_objects
readSequences.AromaCellSequenceFile	Non-documented_objects
readTargetStrands	Non-documented_objects
readTargetStrands.AromaCellSequenceFile	Non-documented_objects
remap	Non-documented_objects
remap.default	Non-documented_objects
reorder.BinnedScatter	Non-documented_objects
require	Non-documented_objects
requireWithMemory	Non-documented_objects
requireWithMemory.default	Non-documented_objects
rescale	Non-documented_objects
rescale.Image	Non-documented_objects
rescale.RasterImage	Non-documented_objects
rgbTransform	Non-documented_objects
rgbTransform.Image	Non-documented_objects
RichDataFrame	Non-documented_objects
SampleAnnotationFile	Non-documented_objects
SampleAnnotationSet	Non-documented_objects
save.RasterImage	Non-documented_objects
SegmentationDataFile	Non-documented_objects
SegmentationDataSet	Non-documented_objects
segmentByCBS	Non-documented_objects
segmentByCBS,RawGenomicSignals-method	segmentByCBS.RawGenomicSignals
segmentByCBS.NonPairedPSCNData	Non-documented_objects
segmentByCBS.PairedPSCNData	Non-documented_objects
segmentByCBS.RawGenomicSignals	segmentByCBS.RawGenomicSignals
segmentByGLAD	Non-documented_objects
segmentByGLAD,RawGenomicSignals-method	segmentByGLAD.RawGenomicSignals
segmentByGLAD.RawGenomicSignals	segmentByGLAD.RawGenomicSignals
segmentByHaarSeg	Non-documented_objects
segmentByHaarSeg,RawGenomicSignals-method	segmentByHaarSeg.RawGenomicSignals
segmentByHaarSeg.RawGenomicSignals	segmentByHaarSeg.RawGenomicSignals
segmentByMPCBS	Non-documented_objects
segmentByMPCBS,RawGenomicSignals-method	segmentByMPCBS.RawGenomicSignals
segmentByMPCBS.RawGenomicSignals	segmentByMPCBS.RawGenomicSignals
segmentByPairedPSCBS	Non-documented_objects
segmentByPairedPSCBS.PairedPSCNData	Non-documented_objects
SegmentedAlleleBFractions	SegmentedAlleleBFractions
SegmentedCopyNumbers	SegmentedCopyNumbers
SegmentedGenomicSignalsInterface	SegmentedGenomicSignalsInterface
setAlias	Non-documented_objects
setAlias,Explorer-method	setAlias.Explorer
setAlias.ChromosomalModel	Non-documented_objects
setAlias.Explorer	setAlias.Explorer
setArrays	Non-documented_objects
setArrays,ChromosomeExplorer-method	setArrays.ChromosomeExplorer
setArrays,Explorer-method	setArrays.Explorer
setArrays.ChromosomeExplorer	setArrays.ChromosomeExplorer
setArrays.Explorer	setArrays.Explorer
setAttributes.RichDataFrame	Non-documented_objects
setAttributesBy.AromaMicroarrayDataSet	Non-documented_objects
setAttributesBy.AromaTabularBinarySet	Non-documented_objects
setAttributesBySampleAnnotationFile	Non-documented_objects
setAttributesBySampleAnnotationFile.AromaMicroarrayDataSet	Non-documented_objects
setAttributesBySampleAnnotationFile.AromaTabularBinarySet	Non-documented_objects
setAttributesBySampleAnnotationSet	Non-documented_objects
setAttributesBySampleAnnotationSet.AromaMicroarrayDataSet	Non-documented_objects
setAttributesBySampleAnnotationSet.AromaTabularBinarySet	Non-documented_objects
setAttributesByTags.AromaMicroarrayDataFile	Non-documented_objects
setAttributesByTags.AromaTabularBinaryFile	Non-documented_objects
setAttributesByTags.AromaTabularBinarySet	Non-documented_objects
setAttributeXY	Non-documented_objects
setAttributeXY.AromaMicroarrayDataFile	Non-documented_objects
setBasicField	Non-documented_objects
setBasicField.RawGenomicSignals	Non-documented_objects
setChipType	Non-documented_objects
setChipType.AbstractCNData	Non-documented_objects
setChromosomes	Non-documented_objects
setChromosomes.ChromosomalModel	getChromosomes.ChromosomalModel
setColumnNamesMap	Non-documented_objects
setColumnNamesMap.RichDataFrame	Non-documented_objects
setColumnNamesTranslator	Non-documented_objects
setColumnNamesTranslator.RichDataFrame	Non-documented_objects
setCytoband	Non-documented_objects
setCytoband.ChromosomeExplorer	Non-documented_objects
setGenome	Non-documented_objects
setGenome.ChromosomalModel	Non-documented_objects
setImageData	Non-documented_objects
setImageData.Image	Non-documented_objects
setImageData.RasterImage	Non-documented_objects
setLocusFields	Non-documented_objects
setLocusFields.RawGenomicSignals	Non-documented_objects
setName.RawGenomicSignals	Non-documented_objects
setName.RichDataFrame	Non-documented_objects
setParallelSafe	Non-documented_objects
setParallelSafe.Explorer	Non-documented_objects
setPlatform	Non-documented_objects
setPlatform.AbstractCNData	Non-documented_objects
setRam	Non-documented_objects
setRam.AromaSettings	Non-documented_objects
setRandomSeed	Non-documented_objects
setRandomSeed.CbsModel	Non-documented_objects
setReference	Non-documented_objects
setReference.CopyNumberChromosomalModel	Non-documented_objects
setReportPathPattern	Non-documented_objects
setReportPathPattern.Explorer	Non-documented_objects
setSigma	Non-documented_objects
setSigma.RawGenomicSignals	Non-documented_objects
setSignals	Non-documented_objects
setSignals.RawGenomicSignals	Non-documented_objects
setStateColorMap	Non-documented_objects
setStateColorMap.SegmentedGenomicSignalsInterface	Non-documented_objects
setStates	Non-documented_objects
setStates.SegmentedGenomicSignalsInterface	Non-documented_objects
setSubname	Non-documented_objects
setSubname.Explorer	Non-documented_objects
setTags.AromaTransform	Non-documented_objects
setTags.RichDataFrame	Non-documented_objects
setup	Non-documented_objects
setup.ChromosomeExplorer	Non-documented_objects
setup.Explorer	Non-documented_objects
setVerbose	Non-documented_objects
setVerbose.AromaRepository	Non-documented_objects
setVerbose.AromaSettings	Non-documented_objects
setVirtualColumn	Non-documented_objects
setVirtualColumn.RichDataFrame	Non-documented_objects
setVirtualColumnFunctions	Non-documented_objects
setVirtualColumnFunctions.RichDataFrame	Non-documented_objects
setWeights	Non-documented_objects
setWeights.RawGenomicSignals	Non-documented_objects
setXScale	Non-documented_objects
setXScale.RawGenomicSignals	Non-documented_objects
setYScale	Non-documented_objects
setYScale.RawGenomicSignals	Non-documented_objects
setZooms	Non-documented_objects
setZooms.ChromosomeExplorer	Non-documented_objects
shakyText	Non-documented_objects
shakyText.default	Non-documented_objects
signalRange	Non-documented_objects
signalRange.RawGenomicSignals	Non-documented_objects
simulateRawCopyNumbers	Non-documented_objects
simulateRawCopyNumbers.CopyNumberRegions	Non-documented_objects
smoothWRMA	Non-documented_objects
smoothWRMA.matrix	Non-documented_objects
smoothWSA	Non-documented_objects
smoothWSA.matrix	Non-documented_objects
sort.RawGenomicSignals	Non-documented_objects
splitByReportPathPattern	Non-documented_objects
splitByReportPathPattern.Explorer	Non-documented_objects
splitInChunks	Non-documented_objects
splitInChunks.numeric	Non-documented_objects
sqrtabs	Non-documented_objects
sqrtcenter	Non-documented_objects
sqrtneg	Non-documented_objects
sqrtpos	Non-documented_objects
sqrtsign	Non-documented_objects
stextChipType	Non-documented_objects
stextChipType.character	Non-documented_objects
stextLabel	Non-documented_objects
stextLabel.AromaMicroarrayDataFile	Non-documented_objects
stextLabels	Non-documented_objects
stextLabels.AromaMicroarrayDataFile	Non-documented_objects
stextSize	Non-documented_objects
stextSize.AromaMicroarrayDataFile	Non-documented_objects
str.RasterImage	Non-documented_objects
stringTree	Non-documented_objects
stringTree.character	Non-documented_objects
subsample	Non-documented_objects
subsample.BinnedScatter	Non-documented_objects
subset.AromaTabularBinaryFile	Non-documented_objects
subset.BinnedScatter	Non-documented_objects
subset.CopyNumberRegions	Non-documented_objects
subset.RichDataFrame	Non-documented_objects
subtractBy	Non-documented_objects
subtractBy.RawGenomicSignals	Non-documented_objects
summary.AromaTabularBinaryFile	Non-documented_objects
summary.RawGenomicSignals	Non-documented_objects
summaryOfUnits	Non-documented_objects
summaryOfUnits.AromaUflFile	Non-documented_objects
text.ProbePositionEffects	Non-documented_objects
textSequence	Non-documented_objects
textSequence.ProbePositionEffects	Non-documented_objects
TextUnitNamesFile	Non-documented_objects
translateColumnNames.RichDataFrame	Non-documented_objects
unique.CopyNumberRegions	Non-documented_objects
UnitAnnotationDataFile	UnitAnnotationDataFile
UnitNamesFile	UnitNamesFile
UnitNamesFile.indexOf	indexOf.UnitNamesFile
UnitTypesFile	UnitTypesFile
updateCpgs	Non-documented_objects
updateCpgs.AromaCellCpgFile	Non-documented_objects
updateData	Non-documented_objects
updateData.AromaTabularBinaryFile	Non-documented_objects
updateDataColumn	Non-documented_objects
updateDataColumn.AromaTabularBinaryFile	Non-documented_objects
updateGenotypes	Non-documented_objects
updateGenotypes.AromaUnitGenotypeCallFile	Non-documented_objects
updatePositions	Non-documented_objects
updatePositions.AromaCellPositionFile	Non-documented_objects
updateSequenceMatrix	Non-documented_objects
updateSequenceMatrix.AromaCellSequenceFile	Non-documented_objects
updateSequences	Non-documented_objects
updateSequences.AromaCellSequenceFile	Non-documented_objects
updateSetupExplorerFile	Non-documented_objects
updateSetupExplorerFile,ChromosomeExplorer-method	updateSetupExplorerFile.ChromosomeExplorer
updateSetupExplorerFile.ChromosomeExplorer	updateSetupExplorerFile.ChromosomeExplorer
updateSetupExplorerFile.Explorer	Non-documented_objects
updateTargetStrands	Non-documented_objects
updateTargetStrands.AromaCellSequenceFile	Non-documented_objects
validate.AromaMicroarrayDataSet	Non-documented_objects
validate.AromaUnitSignalBinarySet	Non-documented_objects
weightedMean	Non-documented_objects
whatDataType	Non-documented_objects
whatDataType.default	Non-documented_objects
write	Non-documented_objects
write.default	Non-documented_objects
write.RasterImage	Non-documented_objects
writeAxesLayers	Non-documented_objects
writeAxesLayers.ChromosomeExplorer	Non-documented_objects
writeCopyNumberRegionLayers	Non-documented_objects
writeCopyNumberRegionLayers.ChromosomeExplorer	Non-documented_objects
writeCytobandLayers	Non-documented_objects
writeCytobandLayers.ChromosomeExplorer	Non-documented_objects
writeDataFrame	Non-documented_objects
writeDataFrame,AromaUnitSignalBinaryFile-method	writeDataFrame.AromaUnitSignalBinaryFile
writeDataFrame,AromaUnitSignalBinarySet-method	writeDataFrame.AromaUnitSignalBinarySet
writeDataFrame,AromaUnitTabularBinaryFile-method	writeDataFrame.AromaUnitTabularBinaryFile
writeDataFrame.AromaUnitFracBCnBinarySet	Non-documented_objects
writeDataFrame.AromaUnitPscnBinarySet	Non-documented_objects
writeDataFrame.AromaUnitSignalBinaryFile	writeDataFrame.AromaUnitSignalBinaryFile
writeDataFrame.AromaUnitSignalBinarySet	writeDataFrame.AromaUnitSignalBinarySet
writeDataFrame.AromaUnitTabularBinaryFile	writeDataFrame.AromaUnitTabularBinaryFile
writeDataFrame.AromaUnitTotalCnBinarySet	Non-documented_objects
writeFooter	Non-documented_objects
writeFooter,AromaTabularBinaryFile-method	writeFooter.AromaTabularBinaryFile
writeFooter.AromaTabularBinaryFile	writeFooter.AromaTabularBinaryFile
writeGraphs	Non-documented_objects
writeGraphs.ChromosomeExplorer	Non-documented_objects
writeGridHorizontalLayers	Non-documented_objects
writeGridHorizontalLayers.ChromosomeExplorer	Non-documented_objects
writeImage	Non-documented_objects
writeImage.Image	Non-documented_objects
writeImage.RasterImage	Non-documented_objects
writeRawCopyNumberLayers	Non-documented_objects
writeRawCopyNumberLayers.ChromosomeExplorer	Non-documented_objects
writeRawFooter	Non-documented_objects
writeRawFooter.AromaTabularBinaryFile	Non-documented_objects
writeRegions	Non-documented_objects
writeRegions.ChromosomeExplorer	Non-documented_objects
writeRegions.CopyNumberSegmentationModel	Non-documented_objects
writeRegions.GladModel	Non-documented_objects
xMax	Non-documented_objects
xMax.CopyNumberRegions	Non-documented_objects
xMax.RawGenomicSignals	Non-documented_objects
xMin	Non-documented_objects
xMin.CopyNumberRegions	Non-documented_objects
xMin.RawGenomicSignals	Non-documented_objects
xmlToList	Non-documented_objects
xmlToList.character	Non-documented_objects
xRange	Non-documented_objects
xRange.CopyNumberRegions	Non-documented_objects
xRange.RawGenomicSignals	Non-documented_objects
xSeq	Non-documented_objects
xSeq.RawGenomicSignals	Non-documented_objects
yellow.colors	Non-documented_objects
yMax	Non-documented_objects
yMax.RawGenomicSignals	Non-documented_objects
yMin	Non-documented_objects
yMin.RawGenomicSignals	Non-documented_objects
yRange	Non-documented_objects
yRange.RawGenomicSignals	Non-documented_objects
[.AromaTabularBinaryFile	Non-documented_objects
[.RasterImage	Non-documented_objects
[.RichDataFrame	Non-documented_objects
[<-.AromaTabularBinaryFile	Non-documented_objects
[[.AromaTabularBinaryFile	Non-documented_objects
[[.RichDataFrame	Non-documented_objects
[[<-.RichDataFrame	Non-documented_objects
