makeGRangesListFromExonFiles {TCGAutils}R Documentation

Read Exon level 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) 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."

Usage

makeGRangesListFromExonFiles(filepaths, sampleNames = NULL,
  fileNames = NULL, rangesColumn = "exon")

Arguments

filepaths

A character vector of valid exon data file paths

sampleNames

A character vector of TCGA barcodes to be applied if not present in the data (default NULL)

fileNames

A character vector of file names as downloaded from the Genomic Data Commons Legacy archive (default NULL)

rangesColumn

(default "exon") A single string indicating the name of the column in the data containing the ranges information

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")


[Package TCGAutils version 1.0.1 Index]