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