aroma.tcga-package	aroma.tcga-package
appendFullNamesTranslatorBySdrfFile	Non-documented_objects
appendFullNamesTranslatorBySdrfFile.GenericDataFileSet	Non-documented_objects
appendFullNamesTranslatorBySdrfFileSet	Non-documented_objects
appendFullNamesTranslatorBySdrfFileSet.GenericDataFileSet	Non-documented_objects
appendFullNameTranslatorBySdrfFile	Non-documented_objects
appendFullNameTranslatorBySdrfFile.FullNameInterface	Non-documented_objects
appendFullNameTranslatorBySdrfFileSet	Non-documented_objects
appendFullNameTranslatorBySdrfFileSet.FullNameInterface	Non-documented_objects
aroma.tcga	aroma.tcga-package
as.character.MultisourceChromosomalModel	Non-documented_objects
as.character.TcgaDccDownloader	Non-documented_objects
BiospecimenCoreResource	Non-documented_objects
BroadAfter5NNTotalCopyNumberTcgaDataFile	Non-documented_objects
BroadAfter5NNTotalCopyNumberTcgaDataFileSet	Non-documented_objects
BroadAlleleSpecificCopyNumberTcgaDataFile	Non-documented_objects
BroadAlleleSpecificCopyNumberTcgaDataFileSet	Non-documented_objects
BroadAlleleSpecificThetaTcgaDataFile	Non-documented_objects
BroadAlleleSpecificThetaTcgaDataFileSet	Non-documented_objects
BroadBirdseedGenotypeTcgaDataFile	Non-documented_objects
BroadBirdseedGenotypeTcgaDataFile.exportGenotypeCallsAndConfidenceScores	exportGenotypeCallsAndConfidenceScores.BroadBirdseedGenotypeTcgaDataFile
BroadBirdseedGenotypeTcgaDataFileSet	Non-documented_objects
BroadTotalCopyNumberTcgaDataFile	Non-documented_objects
BroadTotalCopyNumberTcgaDataFileSet	Non-documented_objects
byPath.MageTabFileSet	Non-documented_objects
byPath.SdrfFileSet	Non-documented_objects
clearCache.MultisourceChromosomalModel	Non-documented_objects
downloadCoreTextFile	Non-documented_objects
downloadCoreTextFile.TcgaDccDownloader	Non-documented_objects
downloadFile	Non-documented_objects
downloadFile.TcgaDccDownloader	Non-documented_objects
downloadFiles	Non-documented_objects
downloadFiles.TcgaDccDownloader	Non-documented_objects
downloadFilesByPattern	Non-documented_objects
downloadFilesByPattern.TcgaDccDownloader	Non-documented_objects
downloadUrl	Non-documented_objects
downloadUrl.TcgaDccDownloader	Non-documented_objects
exportGenotypeCalls	Non-documented_objects
exportGenotypeCalls,HudsonAlphaGenotypeTcgaDataFile-method	exportGenotypeCalls.HudsonAlphaGenotypeTcgaDataFile
exportGenotypeCalls.HudsonAlphaGenotypeTcgaDataFile	exportGenotypeCalls.HudsonAlphaGenotypeTcgaDataFile
exportGenotypeCalls.HudsonAlphaGenotypeTcgaDataFileSet	Non-documented_objects
exportGenotypeCallsAndConfidenceScores	Non-documented_objects
exportGenotypeCallsAndConfidenceScores,BroadBirdseedGenotypeTcgaDataFile-method	exportGenotypeCallsAndConfidenceScores.BroadBirdseedGenotypeTcgaDataFile
exportGenotypeCallsAndConfidenceScores.BroadBirdseedGenotypeTcgaDataFile	exportGenotypeCallsAndConfidenceScores.BroadBirdseedGenotypeTcgaDataFile
exportGenotypeCallsAndConfidenceScores.BroadBirdseedGenotypeTcgaDataFileSet	Non-documented_objects
exportTotal	Non-documented_objects
exportTotal.HarvardTotalCopyNumberTcgaDataFile	Non-documented_objects
exportTotal.HarvardTotalCopyNumberTcgaDataFileSet	Non-documented_objects
exportTotal.MskccTotalCopyNumberTcgaDataFile	Non-documented_objects
exportTotal.MskccTotalCopyNumberTcgaDataFileSet	Non-documented_objects
exportTotalAndFracB	Non-documented_objects
exportTotalAndFracB.BroadAfter5NNTotalCopyNumberTcgaDataFileSet	Non-documented_objects
exportTotalAndFracB.BroadTotalCopyNumberTcgaDataFile	Non-documented_objects
exportTotalAndFracB.BroadTotalCopyNumberTcgaDataFileSet	Non-documented_objects
exportTotalAndFracB.HudsonAlphaBAlleleFreqTcgaDataFile	Non-documented_objects
exportTotalAndFracB.HudsonAlphaBAlleleFreqTcgaDataFileSet	Non-documented_objects
exportTotalAndFracB.HudsonAlphaXYTcgaDataFile	Non-documented_objects
exportTotalAndFracB.HudsonAlphaXYTcgaDataFileSet	Non-documented_objects
extractAlleleSpecificCopyNumbers	Non-documented_objects
extractAlleleSpecificCopyNumbers.BroadAlleleSpecificCopyNumberTcgaDataFile	Non-documented_objects
extractByTcgaType	Non-documented_objects
extractByTcgaType.GenericDataFileSet	Non-documented_objects
extractCalls.BroadBirdseedGenotypeTcgaDataFile	Non-documented_objects
extractCalls.HudsonAlphaGenotypeTcgaDataFile	Non-documented_objects
extractConfidenceScores	Non-documented_objects
extractConfidenceScores.BroadBirdseedGenotypeTcgaDataFile	Non-documented_objects
extractFracB	Non-documented_objects
extractFracB.HudsonAlphaBAlleleFreqTcgaDataFile	Non-documented_objects
extractRawCopyNumbers.MultisourceCopyNumberChromosomalModel	Non-documented_objects
extractRawGenomicSignals.MultisourceChromosomalModel	Non-documented_objects
extractTheta	Non-documented_objects
extractTheta.BroadAlleleSpecificThetaTcgaDataFile	Non-documented_objects
extractTheta.HudsonAlphaXYTcgaDataFile	Non-documented_objects
extractTotalAndFracB	Non-documented_objects
extractTotalAndFracB.BroadAlleleSpecificCopyNumberTcgaDataFile	Non-documented_objects
extractTotalAndFracB.BroadAlleleSpecificThetaTcgaDataFile	Non-documented_objects
extractTotalAndFracB.BroadTotalCopyNumberTcgaDataFile	Non-documented_objects
extractTotalAndFracB.HudsonAlphaXYTcgaDataFile	Non-documented_objects
extractTotalCopyNumbers	Non-documented_objects
extractTotalCopyNumbers.BroadTotalCopyNumberTcgaDataFile	Non-documented_objects
extractTotalCopyNumbers.HarvardTotalCopyNumberTcgaDataFile	Non-documented_objects
extractTotalCopyNumbers.MskccTotalCopyNumberTcgaDataFile	Non-documented_objects
extractTotalLog2CopyNumbers	Non-documented_objects
extractTotalLog2CopyNumbers.HarvardTotalCopyNumberTcgaDataFile	Non-documented_objects
extractTotalLog2CopyNumbers.MskccTotalCopyNumberTcgaDataFile	Non-documented_objects
extractTumorNormalPairs	Non-documented_objects
extractTumorNormalPairs.GenericDataFileSet	Non-documented_objects
findDataSets	Non-documented_objects
findDataSets.TcgaDccData	Non-documented_objects
findDataSets2	Non-documented_objects
findDataSets2.TcgaDccData	Non-documented_objects
fit,MultisourceCopyNumberChromosomalModel-method	fit.MultisourceCopyNumberChromosomalModel
fit.MultisourceChromosomalModel	Non-documented_objects
fit.MultisourceCopyNumberChromosomalModel	fit.MultisourceCopyNumberChromosomalModel
getAccessRoot	Non-documented_objects
getAccessRoot.TcgaDccDownloader	Non-documented_objects
getArchive	Non-documented_objects
getArchive.TcgaDccDownloader	Non-documented_objects
getAsteriskTags.MultisourceChromosomalModel	Non-documented_objects
getBarcodeIdTranslator	Non-documented_objects
getBarcodeIdTranslator.TcgaFullNameTranslators	Non-documented_objects
getBarcodeIdTranslators	Non-documented_objects
getBarcodeIdTranslators.TcgaFullNameTranslators	Non-documented_objects
getBarcodePattern	Non-documented_objects
getBarcodePattern.BiospecimenCoreResource	Non-documented_objects
getBarcodePatterns	Non-documented_objects
getBarcodePatterns.BiospecimenCoreResource	Non-documented_objects
getCenter	Non-documented_objects
getCenter.TcgaDccDownloader	Non-documented_objects
getCenterType	Non-documented_objects
getCenterType.TcgaDccDownloader	Non-documented_objects
getChipType.MultisourceChromosomalModel	Non-documented_objects
getChipTypes.MultisourceChromosomalModel	Non-documented_objects
getChromosomes,MultisourceChromosomalModel-method	getChromosomes.MultisourceChromosomalModel
getChromosomes.MultisourceChromosomalModel	getChromosomes.MultisourceChromosomalModel
getColumnNames.MskccTotalCopyNumberTcgaDataFile	Non-documented_objects
getDataSet	Non-documented_objects
getDataSet.TcgaDccDownloader	Non-documented_objects
getDataSetList	Non-documented_objects
getDataSetList.MultisourceChromosomalModel	Non-documented_objects
getDataSetName	Non-documented_objects
getDataSetName.TcgaDccDownloader	Non-documented_objects
getDataSetPattern	Non-documented_objects
getDataSetPattern.TcgaDccData	Non-documented_objects
getDataSetPatterns	Non-documented_objects
getDataSetPatterns.TcgaDccData	Non-documented_objects
getDataType	Non-documented_objects
getDataType.TcgaDccDownloader	Non-documented_objects
getDefaultFullName.TcgaDataFileSet	Non-documented_objects
getExtensionPattern.BroadAfter5NNTotalCopyNumberTcgaDataFile	Non-documented_objects
getExtensionPattern.BroadAlleleSpecificCopyNumberTcgaDataFile	Non-documented_objects
getExtensionPattern.BroadAlleleSpecificThetaTcgaDataFile	Non-documented_objects
getExtensionPattern.BroadBirdseedGenotypeTcgaDataFile	Non-documented_objects
getExtensionPattern.BroadTotalCopyNumberTcgaDataFile	Non-documented_objects
getExtensionPattern.HarvardTotalCopyNumberTcgaDataFile	Non-documented_objects
getExtensionPattern.HudsonAlphaBAlleleFreqTcgaDataFile	Non-documented_objects
getExtensionPattern.HudsonAlphaGenotypeTcgaDataFile	Non-documented_objects
getExtensionPattern.HudsonAlphaXYTcgaDataFile	Non-documented_objects
getExtensionPattern.TcgaDataFile	Non-documented_objects
getExtractNameByFilename	Non-documented_objects
getExtractNameByFilename.SdrfFile	Non-documented_objects
getFilenameMap	Non-documented_objects
getFilenameMap.SdrfFile	Non-documented_objects
getFilenameMap.SdrfFileSet	Non-documented_objects
getFilenamePattern	Non-documented_objects
getFilenamePattern.BroadAlleleSpecificCopyNumberTcgaDataFile	Non-documented_objects
getFilenamePattern.BroadAlleleSpecificThetaTcgaDataFile	Non-documented_objects
getFilenamePattern.BroadTotalCopyNumberTcgaDataFile	Non-documented_objects
getFilenamePattern.TcgaDataFile	Non-documented_objects
getFullName.MultisourceChromosomalModel	Non-documented_objects
getFullNames.MultisourceChromosomalModel	Non-documented_objects
getFullNameTranslator.MscnExport	Non-documented_objects
getGenome.MultisourceChromosomalModel	Non-documented_objects
getGenomeData.MultisourceChromosomalModel	Non-documented_objects
getGenomeFile.MultisourceChromosomalModel	Non-documented_objects
getHeader.MageTabDataMatrixFile	Non-documented_objects
getKnownFilePatterns	Non-documented_objects
getKnownFilePatterns.TcgaDccDownloader	Non-documented_objects
getName.MultisourceChromosomalModel	Non-documented_objects
getNames,MultisourceChromosomalModel-method	getNames.MultisourceChromosomalModel
getNames.MultisourceChromosomalModel	getNames.MultisourceChromosomalModel
getParentPath.MultisourceChromosomalModel	Non-documented_objects
getPassword	Non-documented_objects
getPassword.TcgaDccDownloader	Non-documented_objects
getPath.MultisourceChromosomalModel	Non-documented_objects
getPlatform.TcgaDccDownloader	Non-documented_objects
getProtocol	Non-documented_objects
getProtocol.TcgaDccDownloader	Non-documented_objects
getReadArguments.BroadAlleleSpecificCopyNumberTcgaDataFile	Non-documented_objects
getReadArguments.BroadAlleleSpecificThetaTcgaDataFile	Non-documented_objects
getReadArguments.BroadBirdseedGenotypeTcgaDataFile	Non-documented_objects
getReadArguments.BroadTotalCopyNumberTcgaDataFile	Non-documented_objects
getReadArguments.HarvardTotalCopyNumberTcgaDataFile	Non-documented_objects
getReadArguments.HudsonAlphaBAlleleFreqTcgaDataFile	Non-documented_objects
getReadArguments.HudsonAlphaGenotypeTcgaDataFile	Non-documented_objects
getReadArguments.HudsonAlphaXYTcgaDataFile	Non-documented_objects
getReadArguments.MageTabDataMatrixFile	Non-documented_objects
getReadArguments.MskccTotalCopyNumberTcgaDataFile	Non-documented_objects
getReportPath.MultisourceChromosomalModel	Non-documented_objects
getRootPath	Non-documented_objects
getRootPath.MultisourceChromosomalModel	Non-documented_objects
getRootPath.TcgaDccDownloader	Non-documented_objects
getRootUrl	Non-documented_objects
getRootUrl.TcgaDccDownloader	Non-documented_objects
getSetTag.MultisourceChromosomalModel	Non-documented_objects
getSetTag.RawMultisourceCopyNumberModel	Non-documented_objects
getTags.MultisourceChromosomalModel	Non-documented_objects
getTumorType	Non-documented_objects
getTumorType.TcgaDccDownloader	Non-documented_objects
getUrl.TcgaDccDownloader	Non-documented_objects
getUrlPath	Non-documented_objects
getUrlPath.TcgaDccDownloader	Non-documented_objects
getUrlPathname	Non-documented_objects
getUrlPathname.TcgaDccDownloader	Non-documented_objects
getUsername.TcgaDccDownloader	Non-documented_objects
HarvardTotalCopyNumberTcgaDataFile	Non-documented_objects
HarvardTotalCopyNumberTcgaDataFileSet	Non-documented_objects
hasFile.TcgaDccDownloader	Non-documented_objects
hasFiles	Non-documented_objects
hasFiles.TcgaDccDownloader	Non-documented_objects
HudsonAlphaBAlleleFreqTcgaDataFile	Non-documented_objects
HudsonAlphaBAlleleFreqTcgaDataFileSet	Non-documented_objects
HudsonAlphaGenotypeTcgaDataFile	Non-documented_objects
HudsonAlphaGenotypeTcgaDataFile.exportGenotypeCalls	exportGenotypeCalls.HudsonAlphaGenotypeTcgaDataFile
HudsonAlphaGenotypeTcgaDataFileSet	Non-documented_objects
HudsonAlphaXYTcgaDataFile	Non-documented_objects
HudsonAlphaXYTcgaDataFileSet	Non-documented_objects
indexOf.MultisourceChromosomalModel	Non-documented_objects
listFiles	Non-documented_objects
listFiles.TcgaDccDownloader	Non-documented_objects
MageTabDataMatrixFile	Non-documented_objects
MageTabDataMatrixFileSet	Non-documented_objects
MageTabFile	Non-documented_objects
MageTabFileSet	Non-documented_objects
makeFullNamesTranslator	Non-documented_objects
makeFullNamesTranslator.SdrfFile	Non-documented_objects
makeFullNamesTranslator.SdrfFileSet	Non-documented_objects
MscnExport	Non-documented_objects
MskccTotalCopyNumberTcgaDataFile	Non-documented_objects
MskccTotalCopyNumberTcgaDataFileSet	Non-documented_objects
MultisourceChromosomalModel	MultisourceChromosomalModel
MultisourceChromosomalModel.getChromosomes	getChromosomes.MultisourceChromosomalModel
MultisourceChromosomalModel.getNames	getNames.MultisourceChromosomalModel
MultisourceChromosomalModel.nbrOfArrays	nbrOfArrays.MultisourceChromosomalModel
MultisourceCopyNumberChromosomalModel	MultisourceCopyNumberChromosomalModel
MultisourceCopyNumberChromosomalModel.fit	fit.MultisourceCopyNumberChromosomalModel
nbrOfArrays,MultisourceChromosomalModel-method	nbrOfArrays.MultisourceChromosomalModel
nbrOfArrays.MultisourceChromosomalModel	nbrOfArrays.MultisourceChromosomalModel
nbrOfSources	Non-documented_objects
nbrOfSources.MultisourceChromosomalModel	Non-documented_objects
Non-documented objects	Non-documented_objects
parseSdrfExtractName	Non-documented_objects
parseTcgaDccArchiveName	Non-documented_objects
parseTcgaDccArchiveName.character	parseTcgaDccArchiveName.character
pruneSDRF	Non-documented_objects
RawMultisourceCopyNumberModel	RawMultisourceCopyNumberModel
readBCRSamplesTable	Non-documented_objects
readBCRSamplesTable.TcgaDccDownloader	Non-documented_objects
readDescription	Non-documented_objects
readDescription.TcgaDccDownloader	Non-documented_objects
readIdf	Non-documented_objects
readIdf.TcgaDccDownloader	Non-documented_objects
readLines	Non-documented_objects
readLines.default	Non-documented_objects
readLines.TcgaDccDownloader	Non-documented_objects
readManifest	Non-documented_objects
readManifest.TcgaDccDownloader	Non-documented_objects
readReadme	Non-documented_objects
readReadme.TcgaDccDownloader	Non-documented_objects
readSampleInfo	Non-documented_objects
readSampleInfo.TcgaDccDownloader	Non-documented_objects
readSdrf	Non-documented_objects
readSdrf.TcgaDccDownloader	Non-documented_objects
readSDRFFile	Non-documented_objects
readSDRFFolder	Non-documented_objects
readTextFile	Non-documented_objects
readTextFile.TcgaDccDownloader	Non-documented_objects
SdrfFile	Non-documented_objects
SdrfFileSet	Non-documented_objects
setFullNamesTranslatorBySdrfFile	Non-documented_objects
setFullNamesTranslatorBySdrfFile.GenericDataFileSet	Non-documented_objects
setFullNamesTranslatorBySdrfFileSet	Non-documented_objects
setFullNamesTranslatorBySdrfFileSet.GenericDataFileSet	Non-documented_objects
setGenome.MultisourceChromosomalModel	Non-documented_objects
setLogin	Non-documented_objects
setLogin.TcgaDccDownloader	Non-documented_objects
setName.MultisourceChromosomalModel	Non-documented_objects
setPassword	Non-documented_objects
setPassword.TcgaDccDownloader	Non-documented_objects
setUsername	Non-documented_objects
setUsername.TcgaDccDownloader	Non-documented_objects
TcgaDataFile	Non-documented_objects
TcgaDataFileSet	Non-documented_objects
TcgaDccData	Non-documented_objects
TcgaDccDownloader	Non-documented_objects
tcgaDccFullnameTranslator	Non-documented_objects
tcgaDccFullnameTranslator.character	tcgaDccFullnameTranslator.character
TcgaFullNameTranslators	Non-documented_objects
