splitROIs: Split (larger) ROIs into multiple smaller (overlapping) bins...

In bioinf-jku/panelcn.mops: CNV detection tool for targeted NGS panel data

Split (larger) ROIs into multiple smaller (overlapping) bins and create new BED file

Description

Split (larger) ROIs into multiple smaller (overlapping) bins and create new BED file

Usage

splitROIs(oldBedFile, newBedFile, limit = 0, bin = 100, shift = 50,
  chr = FALSE)

Arguments

oldBedFile	filename of the BED file with absolute or relative path (structure of BED file without header: chromosome, exon start, exon end, exon name)
newBedFile	filename of the new BED file that should be created
limit	ROIs larger than limit will be split
bin	size of bins (in bp) the ROIs will be split into
shift	no. of bp between start positions of adjacent bins
chr	indicates whether naming contains chr prefix

Value

generates a new BED file with (larger) ROIs split into smaller bins

Examples

bed <- list.files(system.file("extdata", package = "panelcn.mops"),
                    pattern = ".bed$", full.names = TRUE)
splitROIs(bed, "newBed.bed")

bioinf-jku/panelcn.mops documentation built on March 24, 2022, 1:19 a.m.