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