circ.chromo.plot: Circos plot combining segmentation and SV calls

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

Description

Circos plot combining segmentation and SV calls

Usage

circ.chromo.plot(
  chromo.regs.obj,
  sample.id,
  genome.v = "hg19",
  lrr.pct = 0.2,
  lrr.max = 4,
  chrlist = NULL,
  ...
)

Arguments

chromo.regs.obj	(chromo.regs) An object of class chromo.regs
sample.id	(character) the id of a sample to be plotted within
genome.v	(hg19 or h38) reference genome version to draw chromosome limits and centromeres
lrr.pct	(numeric) copy number change between 2 consecutive segments: i.e (default) cutoff = 0.2 represents 20 percent fold change
lrr.max	(numeric) CNV plot limit
chrlist	(character) vector containing chromosomes to plot; by default only chromosomes with shattered regions are ploted

Value

circos plot into open device

Examples

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

## obtain shattered regions
shatt.regions <- shattered.regions(cnv,svc)

# select a random sample from the 
id <- "SCLC21H_LUNG"

circ.chromo.plot(shatt.regions, sample.id = id)

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