TCGA utility functions for data management

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Documentation for package ‘TCGAutils’ version 1.0.1

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TCGAutils-package TCGAutils: Helper functions for working with TCGA and MultiAssayExperiment data
barcodeToUUID Translate study identifiers from barcode to UUID and vice versa
clinicalNames Clinical dataset names in TCGA
curatedTCGAData-helpers Helper functions for managing MultiAssayExperiment from curatedTCGAData
diseaseCodes TCGA Cancer Disease Codes Table
extractBuild Translate study identifiers from barcode to UUID and vice versa
findGRangesCols Obtain minimum necessary names for the creation of a GRangesList object
generateMap Create a sampleMap from an experiment list and phenoData dataframe
getClinicalNames Helper functions for managing MultiAssayExperiment from curatedTCGAData
getFileNames Find the file names used in RTCGAToolbox
getSubtypeMap Helper functions for managing MultiAssayExperiment from curatedTCGAData
ID-translation Translate study identifiers from barcode to UUID and vice versa
makeGRangesListFromCopyNumber Make a GRangesList from TCGA Copy Number data
makeGRangesListFromExonFiles Read Exon level files and create a GRangesList
makeSummarizedExperimentFromGISTIC Create a SummarizedExperiment from FireHose GISTIC
mergeColData Take a MultiAssayExperiment and include curated variables
sampleTables Helper functions for managing MultiAssayExperiment from curatedTCGAData
sampleTypes Barcode Sample Type Table
splitAssays Helper functions for managing MultiAssayExperiment from curatedTCGAData
TCGAbarcode Parse data from TCGA barcode
TCGAbiospec Extract biospecimen data from the TCGA barcode
TCGAsampleSelect Select samples from barcodes from lookup table
TCGAutils TCGAutils: Helper functions for working with TCGA and MultiAssayExperiment data
translateBuild Translate study identifiers from barcode to UUID and vice versa
UUIDtoBarcode Translate study identifiers from barcode to UUID and vice versa