plot_cnv: Plot Copy Number Variations

In gsrc: Genome Structure Rearrangement Calling in Genomes with High Synteny

Description

Plots copy number variations in a grid to allow for comparisons between individuals. Deletions and duplications are represented in red and green, respectively.

Usage

plot_cnv(dat, lwd = 1, col = grDevices::rgb(0, 0, 0, 0.5), x.cex = 1,
  y.cex = 1, ...)

Arguments

dat	List object, containing vectors samples, pos and chr and matrix cnv.
lwd	Line width for raster.
col	Color of raster lines.
x.cex	Character size in x-axis.
y.cex	Character size in y-axis.
...	are forwarded to the image() command.

Examples

## Not run: 
if(require(brassicaData)){
data(raw_napus, package = "brassicaData", envir = environment())
raw_napus <- filt_samp(raw_napus, raw_napus$samples[-(1:10)])
raw_napus <- filt_snps(raw_napus, raw_napus$snps[-(1:100)][-(30000:30100)])
dat <- intens_theta(raw_napus)
dat <- remove_suffix(dat, "_Grn")
dat <- geno_baf_rratio(dat, delthresh = 11)
dat <- segm(dat)
dat <- cnv(dat, dup = 0.03, del = -0.06)
plot_cnv(dat)
}

## End(Not run)

Example output

Loading required package: brassicaData
Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'brassicaData'

gsrc documentation built on May 30, 2017, 4:16 a.m.