break.density: Generating a genomic map based on a defined bin size and...

In gonzolgarcia/svcnvplus: Integrative analyses of CNV segmentation and SV variant calls

Description

Generating a genomic map based on a defined bin size and sliding window and counts the number of breakpoints mapped onto each bin. This function is used internally by svpluscnv::shattered.regions and svpluscnv::shattered.regions.cnv

Usage

break.density(
  brk,
  chr.lim = NULL,
  genome.v = "hg19",
  window.size = 10,
  slide.size = 2,
  verbose = TRUE
)

Arguments

brk	(breaks) An instance of the class 'breaks' obtained from CNV segmentation data (svpluscnv::cnv.breaks) or Structural Variant calls (svpluscnv::svc.breaks).
chr.lim	(data.frame) 3 column table (chrom, begin, end) indicating the chromosome most distal coordinates with coverage. Also returned by the function svpluscnv::chromosome.limit.coords.
genome.v	(hg19 or hg38) reference genome version to draw chromosome limits and centromeres
window.size	(numeric) size in megabases of the genmome bin onto which breakpoints will be mapped
slide.size	(numeric) size in megabases of the sliding genomic window; if slide.size < window.size the genomic bins will overlap
verbose	(logical)

Value

a matrix of samples (rows) and genomic bins (cols) qith the number of breakpoints mapped in heach cell

Examples

cnv <- validate.cnv(segdat_lung_ccle)
brk <- cnv.breaks(cnv)
chr.lim <- chromosome.limit.coords(cnv)
break.density(brk,chr.lim)

gonzolgarcia/svcnvplus documentation built on March 4, 2020, 6:02 p.m.