aroma.tcga: Methods for accessing online The Cancer Genome Atlas (TCGA) data

Utility functions for accessing the public and protected data files at the The Cancer Genome Atlas (TCGA) Data Collection Center (DCC). This package is very much in an alpha stage where the API keeps changing from day to day.

AuthorHenrik Bengtsson <henrikb@braju.com>
Bioconductor views DataImport Infrastructure
Date of publication2010-04-05 15:59:58
MaintainerHenrik Bengtsson <henrikb@braju.com>
LicenseLGPL (>= 2.1)
Version0.5.3
http://www.aroma-project.org/

View on R-Forge

Functions

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

Files

DESCRIPTION
NAMESPACE
R
R/000.R R/006.fixVarArgs.R R/999.NonDocumentedObjects.R R/999.package.R R/BiospecimenCoreResource.R R/BroadAfter5NNTotalCopyNumberTcgaDataFile.R R/BroadAfter5NNTotalCopyNumberTcgaDataFileSet.R R/BroadAlleleSpecificCopyNumberTcgaDataFile.R R/BroadAlleleSpecificCopyNumberTcgaDataFileSet.R R/BroadAlleleSpecificThetaTcgaDataFile.R R/BroadAlleleSpecificThetaTcgaDataFileSet.R R/BroadBirdseedGenotypeTcgaDataFile.R R/BroadBirdseedGenotypeTcgaDataFile.exportGenotypeCallsAndConfidenceScores.R R/BroadBirdseedGenotypeTcgaDataFileSet.R R/BroadTotalCopyNumberTcgaDataFile.R R/BroadTotalCopyNumberTcgaDataFile.exportTotalAndFracB.R R/BroadTotalCopyNumberTcgaDataFileSet.R R/BroadTotalCopyNumberTcgaDataFileSet.exportTotalAndFracB.R R/GenericDataFileSet.XTRAS.R R/HarvardTotalCopyNumberTcgaDataFile.R R/HarvardTotalCopyNumberTcgaDataFileSet.R R/HudsonAlphaBAlleleFreqTcgaDataFile.R R/HudsonAlphaBAlleleFreqTcgaDataFileSet.R R/HudsonAlphaGenotypeTcgaDataFile.R R/HudsonAlphaGenotypeTcgaDataFile.exportGenotypeCalls.R R/HudsonAlphaGenotypeTcgaDataFileSet.R R/HudsonAlphaXYTcgaDataFile.R R/HudsonAlphaXYTcgaDataFileSet.R R/MageTabDataMatrixFile.R R/MageTabDataMatrixFileSet.R R/MageTabFile.R R/MageTabFileSet.R R/MscnExport.R R/MskccTotalCopyNumberTcgaDataFile.R R/MskccTotalCopyNumberTcgaDataFileSet.R R/MultisourceChromosomalModel.R R/MultisourceCopyNumberChromosomalModel.R R/RawMultisourceCopyNumberModel.R R/SdrfFile.R R/SdrfFileSet.R R/TcgaDataFile.R R/TcgaDataFileSet.R R/TcgaDccData.R R/TcgaDccData.findDataSets.R R/TcgaDccDownloader.R R/TcgaDccDownloader.readBCRSamplesTable.R R/TcgaFullNameTranslators.R R/parseSdrfExtractName.R R/parseTcgaDccArchiveName.R R/pruneSDRF.R R/readSDRFFile.R R/readSDRFFolder.R R/tcgaDccFullnameTranslator.R R/zzz.R
incl
incl/999.missingdocs.txt
inst
inst/NEWS
inst/testScripts
inst/testScripts/system
inst/testScripts/system/A1.download
inst/testScripts/system/A1.download/1.buildDirectoryStubs.Rex
inst/testScripts/system/A1.download/2.download.Rex
inst/testScripts/system/A1.download/3.downloadBCRTable.Rex
inst/testScripts/system/A1.download/TCGA,DCC,dirs,GBM.txt
inst/testScripts/system/A1.download/TCGA,DCC,dirs,OV.txt
inst/testScripts/system/A2.createLinks
inst/testScripts/system/A2.createLinks/1.LinkRawDataToTCGAData.Rex
inst/testScripts/system/A3.import
inst/testScripts/system/A3.import/1.import.Rex
inst/testScripts/system/A4.CRMAv2
inst/testScripts/system/A4.CRMAv2/1.ASCRMAv2.Rex
inst/testScripts/system/A4.CRMAv2/3.import.Rex
inst/testScripts/system/B1.normalize
inst/testScripts/system/B1.normalize/1.PrincipalCurveNormalization.Rex
inst/testScripts/system/B1.ratios
inst/testScripts/system/B1.ratios/1.CalculateTumorNormalCnRatios.Rex
inst/testScripts/system/B2.QC
inst/testScripts/system/B2.QC/1.PairedTumorNormalBAFs.Rex
inst/testScripts/system/D1.scan
inst/testScripts/system/D1.scan/1.msTabulate.Rex
inst/testScripts/system/D2.MSCN
inst/testScripts/system/D2.MSCN/1.MSCN,batch.Rex
inst/testScripts/system/D2.MSCN/1.MSCN,presmooting.Rex
inst/testScripts/system/D2.MSCN/2.MSCN,subset.Rex
inst/testScripts/system/D4.QC
inst/testScripts/system/D4.QC/1.MSCN,QC,tracks.Rex
inst/testScripts/system/D9.export
inst/testScripts/system/D9.export/1.export.Rex
inst/testScripts/system/E1.segmentation
inst/testScripts/system/E1.segmentation/1.CBS,subset.Rex
inst/testScripts/system/qc
inst/testScripts/system/qc/test20090930,MSCN,QC,tracks.Rex
inst/testScripts/system/scan
inst/testScripts/system/scan/test20090929,findSamples.Rex
man
man/MultisourceChromosomalModel.Rd man/MultisourceCopyNumberChromosomalModel.Rd man/Non-documented_objects.Rd man/RawMultisourceCopyNumberModel.Rd man/aroma.tcga-package.Rd man/exportGenotypeCalls.HudsonAlphaGenotypeTcgaDataFile.Rd man/exportGenotypeCallsAndConfidenceScores.BroadBirdseedGenotypeTcgaDataFile.Rd man/fit.MultisourceCopyNumberChromosomalModel.Rd man/getChromosomes.MultisourceChromosomalModel.Rd man/getNames.MultisourceChromosomalModel.Rd man/nbrOfArrays.MultisourceChromosomalModel.Rd man/parseTcgaDccArchiveName.character.Rd man/tcgaDccFullnameTranslator.character.Rd

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