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

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Files in this package

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

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