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

In waldronlab/TCGAutils: TCGA utility functions for data management

Read exon-level expression files and create a GRangesList

Description

This function serves to read exon-level expression data. It works for exon quantification (raw counts and RPKM) and junction quantification (raw counts) file paths and represents such data as a GRangesList. The data files can be downloaded via the Genomic Data Commons (GDC) Legacy Archive.

Usage

makeGRangesListFromExonFiles(
  filepaths,
  sampleNames = NULL,
  fileNames = basename(filepaths),
  getBarcodes = TRUE,
  rangesColumn = "exon",
  nrows = Inf
)

Arguments

filepaths	character() vector of file paths containing TCGA exon data usually obtained from the GDC
sampleNames	character() vector of TCGA barcodes to be used as names for the GRangesList output (default NULL)
fileNames	character() vector of file names as downloaded from the Genomic Data Commons Legacy archive (default basename(filepaths))
getBarcodes	logical(1). Whether to query the GDC API with the filenameToBarcode and obtain the TCGA barcodes from the file names (default TRUE); see details.
rangesColumn	character(1). The name of the column in the data containing the ranges information (default "exon"); see details.
nrows	numeric(1). The number of rows to return from each of the files read in (all rows by default; default Inf)

Details

The rangesColumn name in the GDC data files is usually "exon" but can be changed with the rangesColumn argument, if different. To avoid programmatically obtaining TCGA barcodes from the GDC API, set the getBarcodes to FALSE. When getBarcodes is set to FALSE, the file names are used to name the elements of the GRangesList output.

Value

A GRangesList object

Author(s)

M. Ramos

Examples

## Load example file found in package
pkgDir <- system.file("extdata", package = "TCGAutils", mustWork = TRUE)
exonFile <- list.files(pkgDir, pattern = "cation\\.txt$", full.names = TRUE)

filePrefix <- "unc.edu.32741f9a-9fec-441f-96b4-e504e62c5362.1755371."

## Add actual file name manually (due to Windows OS restriction)
makeGRangesListFromExonFiles(exonFile,
    fileNames = paste0(filePrefix, basename(exonFile)),
    sampleNames = "TCGA-AA-3678-01A-01R-0905-07")

waldronlab/TCGAutils documentation built on Feb. 25, 2024, midnight