plotChrCNV: Generate chromosome-level CNV plot of given sample

In hshdndx/new-to-CNV: patternCNV: a versatile tool for detecting copy number changes from exome-seq data

Description

This function generates chromosome-level CNV plot of given sample.

Usage

plotChrCNV(data.name, sample.name, sel.chr = "chr1", pos.range = NULL, 
                  capture.only = TRUE, min.ref.avgRPKM = 2, ref.avg.method = "median", 
                  cex = 0.65, col = "steelblue3", ylim = c(-3, 3), 
                  xlab = "Mb", ylab = "log2-ratio", 
                  ideogram = FALSE, ideogram.cex = 0.75, ...)

Arguments

data.name	an object of PatCNVData-class
sample.name	character of selected sample name
sel.chr	selected chromosome
pos.range	numeric vector of length 2 containing start and stop positions of chromosome range
capture.only	a logical value indicating if only captured exons should be outputted
min.ref.avgRPKM	minimum normalized coverage of output exons
ref.avg.method	a character indicating if exon-level "median" or "mean" coverage information should be outputted in the table
cex	plot expansion factor relative to current par("cex")
col	color of the plot
ylim	the y limits of the plot
xlab	a title for the x axis
ylab	a title for the y axis
ideogram	a logical value indicating if ideogram of corresponding chromsome should be plotted
ideogram.cex	plot expansion factor relative to current par("cex") for plotting ideogram
...	other graphical parameters (see par)

Author(s)

Chen Wang

See Also

plot autosome CNV results plotAutosomeCNV

Examples

#=== load simulated data with pre-computed coverage and CNV
data(sim.cnvData)

#=== plot CNV of sample "c2" in selected region in "chr22"
plotChrCNV(sim.cnvData,"c2","chr22",c(41e6,44e6),cex=1.2)

#=== plot CNV of sample "n3" in selected region in "chr22"
plotChrCNV(sim.cnvData,"n3","chr22",c(41e6,44e6),cex=1.2)

hshdndx/new-to-CNV documentation built on May 17, 2019, 5:55 p.m.