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 |