plotAutosomeCNV: Generate autosome (chr1-22) 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 autosome (chr1-22) CNV plot of given sample, by connecting CNV values of all the chromosomes

Usage

plotAutosomeCNV(data.name, sample.name, chr.Len.vec, 
                       capture.only = TRUE, min.ref.avgRPKM = 2, 
                       ref.avg.method = "median", ylim = c(-3, 3), cex = 0.6, 
                       xlab = "Mb", ylab = "log2-ratio", 
                       color.vec = c("red", "blue", "green", "orange", "brown",
                       "purple", "black"), ...)

Arguments

data.name	an object of PatCNVData-class
sample.name	character of selected sample name
chr.Len.vec	a numerical vector recording length of 22 chromosomes
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
ylim	the y limits of the plot
cex	plot expansion factor relative to current par("cex")
xlab	a title for the x axis
ylab	a title for the y axis
color.vec	a character vector of colors used to draw CNV of different chromosomes
...	other graphical parameters (see par)

Author(s)

Chen Wang

See Also

plot CNV results of given chromosome plotChrCNV

Examples

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

#=== load a numeric vector "hg19.Chr_length_vec" recording length of 22 autosome
data("hg19.Chr_length_vec",package="patternCNV")

#=== plot whole-exome CNV of sample "n3"
#=== only part of chr-22 is expected to be seen as this is according to the simulation
plotAutosomeCNV(sim.cnvData,"n3",hg19.Chr_length_vec)

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