makeGRangesListFromExonFiles {TCGAutils} | R Documentation |
This function serves to read exon-level expression data. It works for exon quantification (raw counts and RPKM) and junction quantification (raw counts) files paths and represent such data as a GRangesList. The data can be downloaded via the TCGA Legacy Archive. File name and structure requirements are as follows: The third position delimited by dots (".") in the file name should be the universally unique identifier (UUID). The column containing the ranged information is labeled "exon."
makeGRangesListFromExonFiles(filepaths, sampleNames = NULL, fileNames = NULL, rangesColumn = "exon", nrows = Inf)
filepaths |
A |
sampleNames |
A |
fileNames |
A |
rangesColumn |
(default "exon") A single string indicating the name of the column in the data containing the ranges information |
nrows |
The number of rows to return from each of the files read in (all rows by default) |
A GRangesList object
M. Ramos
## 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")