importBed: importBed

In BIMSBbioinfo/RCAS: RNA Centric Annotation System

importBed

Description

This function uses rtracklayer::import.bed() function to import BED files

Usage

importBed(filePath, sampleN = 0, keepStandardChr = TRUE, debug = TRUE, ...)

Arguments

filePath	Path to a BED file
sampleN	A positive integer value. The number of intervals in the input BED file are randomly downsampled to include intervals as many as sampleN. The input will be downsampled only if this value is larger than zero and less than the total number of input intervals.
keepStandardChr	TRUE/FALSE (default:TRUE). If set to TRUE, will convert the seqlevelsStyle to 'UCSC' and apply keepStandardChromosomes function to only keep data from the standard chromosomes
debug	TRUE/FALSE (default:TRUE). Set to FALSE to turn off messages
...	Other arguments passed to rtracklayer::import.bed function

Value

A GRanges object containing the coordinates of the intervals from an input BED file

Examples

input <- system.file("extdata", "testfile.bed", package='RCAS')
importBed(filePath = input, keepStandardChr = TRUE)

BIMSBbioinfo/RCAS documentation built on Feb. 7, 2024, 4:38 p.m.