Package index • TCGAutils

All functions

UUIDtoBarcode() UUIDtoUUID() barcodeToUUID() filenameToBarcode() UUIDhistory(): Translate study identifiers from barcode to UUID and vice versa

TCGAbarcode(): Parse data from TCGA barcode

TCGAbiospec(): Extract biospecimen data from the TCGA barcode

TCGAprimaryTumors(): Select primary tumors from TCGA datasets

TCGAsampleSelect(): Select samples from barcodes from lookup table

TCGAutils TCGAutils-package: TCGAutils: Helper functions for working with TCGA and MultiAssayExperiment data

translateBuild() correctBuild() isCorrect() extractBuild() uniformBuilds(): Utilities for working with HUMAN genome builds

clinicalNames: Clinical dataset names in TCGA

getSubtypeMap() getClinicalNames() TCGAsplitAssays() sampleTables(): Helper functions for managing MultiAssayExperiment from curatedTCGAData

diseaseCodes: TCGA Cancer Disease Codes Table

findGRangesCols(): Obtain minimum necessary names for the creation of a GRangesList object

generateMap(): Create a sampleMap from an experiment list and phenoData dataframe

getFileName(): Find the file names used in RTCGAToolbox

imputeAssay(): This function imputes assays values inside a MultiAssayExperiment

makeGRangesListFromCopyNumber(): Make a GRangesList from TCGA Copy Number data

makeGRangesListFromExonFiles(): Read exon-level expression files and create a GRangesList

mergeColData(): Take a MultiAssayExperiment and include curated variables

oncoPrintTCGA(): OncoPrint for TCGA Mutation Assays

sampleTypes: Barcode Sample Type Table

simplifyTCGA() symbolsToRanges() mirToRanges() CpGtoRanges() qreduceTCGA(): Functions to convert rows annotations to ranges and RaggedExperiment to RangedSummarizedExperiment

trimColData(): Minimize the number of variables in colData