TCGA utility functions for data management


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Documentation for package ‘TCGAutils’ version 1.2.2

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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 Utilities for working with build numbers
filenameToBarcode 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
imputeAssay This function imputes assays values inside a 'MultiAssayExperiment'
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
mirToRanges Convert SummarizedExperiment elements with microRNA to RangedSummarizedExperiment
qreduceTCGA Simplify curatedTCGAData objects by replacing RaggedExperiment objects
sampleTables Helper functions for managing MultiAssayExperiment from curatedTCGAData
sampleTypes Barcode Sample Type Table
simplifyTCGA All-in-one simplification of curatedTCGAData objects
splitAssays Helper functions for managing MultiAssayExperiment from curatedTCGAData
symbolsToRanges Convert SummarizedExperiment elements with gene symbols to RangedSummarizedExperiment
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 Utilities for working with build numbers
uniformBuilds Utilities for working with build numbers
UUIDtoBarcode Translate study identifiers from barcode to UUID and vice versa
UUIDtoUUID Translate study identifiers from barcode to UUID and vice versa