bed2chromo.reg: Transforms a bed format data.frame containing genomic regions...

In ccbiolab/svpluscnv: svpluscnv: analysis and visualization of complex structural variation data

Description

Transforms a bed format data.frame containing genomic regions into a matrix of n samples versus m defined genomic bins where bins overlapping with bed segments take value = 1

Usage

bed2chromo.reg(
  bed,
  bingr = NULL,
  genome.v = "hg19",
  window.size = 10,
  slide.size = 2
)

Arguments

bed	(data.frame) An data.frame
bingr	(S4) a GenomicRanges object containing the
genome.v	(hg19 or hg38) reference genome version to generate genoic bins (ignored if bingr is not NULL)
window.size	(numeric) size in megabases to generate genomic bins
slide.size	(numeric) size in megabases of the sliding genomic window; slide.size must be <= 1

Value

an instance of the class 'chromo.regs' containing information about shattered regions

ccbiolab/svpluscnv documentation built on Sept. 9, 2020, 4:52 a.m.