plotChrCNV: Generate chromosome-level CNV plot of given sample

Description Usage Arguments Author(s) See Also Examples

View source: R/plotChrCNV.R

Description

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

Usage

1
2
3
4
5
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

1
2
3
4
5
6
7
8
#=== 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 16, 2017, 11:26 p.m.