cnv.freq: Plot CNV frequency across the genome using a CNV segmentation...

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

Description

Plot CNV frequency across the genome using a CNV segmentation file containing multiple samples

Usage

cnv.freq(
  cnv,
  fc.pct = 0.2,
  genome.v = "hg19",
  ploidy = FALSE,
  g.bin = 1,
  sampleids = NULL,
  cex.axis = 1,
  cex.lab = 1,
  label.line = -1.2,
  plot = TRUE,
  summary = TRUE,
  verbose = TRUE
)

Arguments

cnv	(S4) an object of class svcnvio containing data type 'cnv' validated by validate.cnv
fc.pct	(numeric) percentage CNV gain/loss for a segment to be considered changed (i.e. 0.2 = 20 percent change 0.8 < segmean && segmean > 1.2)
genome.v	(hg19 or h38) reference genome version to draw chromosome limits and centromeres
g.bin	(numeric) size in megabases of the genome bin to compute break density
sampleids	(character) vector containing list of samples to include in plot. if set to NULL, all samples in the input will be used
cex.axis, cex.lab, label.line	(numeric) plot parameters
plot	(logical) whether to produce a graphical output
summary	(logical) whether to return an object with a summary
verbose	(logical)

Value

an instance of the class 'cnvfreq' and optionally a plot into open device

Examples

## validate input data.frame
cnv <- validate.cnv(nbl_segdat)

cnv.freq(cnv, genome.v = "hg19")

gonzolgarcia/svpluscnv documentation built on March 4, 2020, 10:06 a.m.