TCGA utility functions for data management

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Documentation for package ‘TCGAutils’ version 1.24.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
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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
builds	Utilities for working with _HUMAN_ genome builds
clinicalNames	Clinical dataset names in TCGA
correctBuild	Utilities for working with _HUMAN_ genome builds
CpGtoRanges	Functions to convert rows annotations to ranges and RaggedExperiment to RangedSummarizedExperiment
curatedTCGAData-helpers	Helper functions for managing MultiAssayExperiment from curatedTCGAData
diseaseCodes	TCGA Cancer Disease Codes Table
extractBuild	Utilities for working with _HUMAN_ genome builds
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
getFileName	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'
isCorrect	Utilities for working with _HUMAN_ genome builds
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
mirToRanges	Functions to convert rows annotations to ranges and RaggedExperiment to RangedSummarizedExperiment
oncoPrintTCGA	OncoPrint for TCGA Mutation Assays
qreduceTCGA	Functions to convert rows annotations to ranges and RaggedExperiment to RangedSummarizedExperiment
sampleTables	Helper functions for managing MultiAssayExperiment from curatedTCGAData
sampleTypes	Barcode Sample Type Table
simplifyTCGA	Functions to convert rows annotations to ranges and RaggedExperiment to RangedSummarizedExperiment
symbolsToRanges	Functions to convert rows annotations to ranges and RaggedExperiment to RangedSummarizedExperiment
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
TCGAsplitAssays	Helper functions for managing MultiAssayExperiment from curatedTCGAData
TCGAutils	TCGAutils: Helper functions for working with TCGA and MultiAssayExperiment data
translateBuild	Utilities for working with _HUMAN_ genome builds
trimColData	Minimize the number of variables in colData
uniformBuilds	Utilities for working with _HUMAN_ genome builds
UUIDhistory	Translate study identifiers from barcode to UUID and vice versa
UUIDtoBarcode	Translate study identifiers from barcode to UUID and vice versa
UUIDtoUUID	Translate study identifiers from barcode to UUID and vice versa