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.

Author
Henrik Bengtsson <henrikb@braju.com>
Date of publication
2010-04-05 15:59:58
Maintainer
Henrik Bengtsson <henrikb@braju.com>
License
LGPL (>= 2.1)
Version
0.5.3
URLs

View on R-Forge

Man pages

aroma.tcga-package
Package aroma.tcga
exportGenotypeCallsAndConfidenceScores.BroadBirdseedGenotypeTcgaDataFile
Exports genotype calls and confidence scores
exportGenotypeCalls.HudsonAlphaGenotypeTcgaDataFile
Exports genotype calls and confidence scores
fit.MultisourceCopyNumberChromosomalModel
Fits the model
getChromosomes.MultisourceChromosomalModel
Gets the chromosomes available
getNames.MultisourceChromosomalModel
Gets the names of the arrays
MultisourceChromosomalModel
The MultisourceChromosomalModel class
MultisourceCopyNumberChromosomalModel
The MultisourceCopyNumberChromosomalModel class
nbrOfArrays.MultisourceChromosomalModel
Gets the number of arrays
Non-documented_objects
Non-documented objects
parseTcgaDccArchiveName.character
Parses a TCGA DCC archive name
RawMultisourceCopyNumberModel
The RawMultisourceCopyNumberModel class
tcgaDccFullnameTranslator.character
Translates a TCGA DCC fullname

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