cnv.freq: CNV frequency map

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

Description

Creates a map of CNVs using genome binning and plots CNV frequency across the genome. This function optionally returns text, graphical or both outputs. Additionaly, calculates the proportion of samples with a given percentage of chromosome arm gained/lost

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,
  verbose = TRUE
)

Arguments

cnv	(S4) an object of class svcnvio containing data type 'cnv' initialized 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	(character) (hg19 or h38) reference genome version to draw chromosome limits and centromeres
ploidy	(logical) whether to apply ploidy correction; the function med.segmean will be used to obtain each sample's ploidy logR then this value substracted to each sample's logR values
g.bin	(numeric) size in megabases of the genmome 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 produce a graphical output
verbose	(logical) whether to return internal messages

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")

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