shattered.map.plot: Shattered regions genomic map

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

Description

Plots a genome wide map of shattered region frequencies

Usage

shattered.map.plot(
  chromo.regs.obj,
  conf = "hc",
  genome.v = "hg19",
  chrlist = NULL,
  freq.cut = NULL,
  add.legend = "top"
)

Arguments

chromo.regs.obj	(chromo.regs) An object of class chromo.regs
conf	(character) either 'hc' for high confidence objects or else all included
genome.v	(character) reference genome version to draw chromosome limits and centromeres either hg19 or hg38 accepted
chrlist	(character) vector containing chromosomes to include in the analysis; if NULL all chromosomes available in the input will be included
freq.cut	the value to draw an horizontal line; use 'freq.p.test' to obtain a threshold for statisticaly significant hot spots
add.legend	the position of the legend in the plot; if null, no legend will be draw

Value

a plot into open device

Examples

## validate input data.frames
cnv <- validate.cnv(segdat_lung_ccle)
svc <- validate.svc(svdat_lung_ccle)

## obtain shattered regions
chromo.regs.obj <- shattered.regions(cnv,svc)

shattered.map.plot(chromo.regs.obj)

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