Category and Function Description
MultiAssayExperiment helpers
generateMap Automatically generate a sampleMap structure from assays
imputeAssay Impute values in numerical assays based on KNN
mergeColData Add additional data to the colData slot of MAE
qreduceTCGA Convert RaggedExperiment assays to RSE based on heuristics
symbolsToRanges Convert gene symbols to genomic ranges using org.db
mirToRanges Convert microRNA sequences to genomic ranges with mirbase.db
simplifyTCGA Use qreduceTCGA, symbolsToRanges, and mirToRanges in succession
curatedTCGAData helpers
getSubtypeMap Obtain the available subtype information
getClinicalNames Get a list of clinical variable names for all cancer types
splitAssays Separate assays based on sample data found in barcodes
sampleTables Get a list of samples in each assay in a MAE
TCGAprimaryTumors Select only primary tumors from TCGA data barcodes
oncoPrintTCGA Produce an oncoPrint plot from TCGA mutation data
TCGA Identifiers
TCGAbarcode Chop TCGA barcode into sections
TCGAbiospec Get a table of information extracted from a vector of barcodes
TCGAsampleSelect Indicate which barcodes belong to a specific sample type
UUIDtoBarcode Translate universal identifiers to TCGA barcodes
UUIDtoUUID Translate between case and file universal identifiers
barcodeToUUID Translate TCGA barcodes to universal identifiers
filenameToBarcode Obtain TCGA barcodes from a vector of TCGA file names
Flat to Bioconductor classes
makeGRangesListFromCopyNumber Create a GRangesList from a copy number data.frame
makeGRangesListFromExonFiles Obtain a GRangesList object from a list of in dividual exon files
makeSummarizedExperimentFromGISTIC Create a SummarizedExperiment object from a Firehose GISTIC RTCGAToolbox object
Genome Builds
translateBuild Translate build version name between UCSC and NCBI
extractBuild Find build in string pattern such as a file name
uniformBuilds Homogenize a vector of builds based on a threshold for the alternative build name
Reference data
diseaseCodes Get a table of TCGA cancer codes and subtype availability
sampleTypes Get a table of sample type codes and their definition
clinicalNames Obtain a CharacterList of common variable names for each TCGA disease code
getFilename Obtain a file name string for the relevant data query
Miscellaneous
findGRangesCols Find the minimum necessary variable names for conversion to GRanges