plotGeneHeatmap: Generate CNV heatmap of given genes

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

Description

This function generates CNV heatmap of given genes.

Usage

plotGeneHeatmap(data.name, sel.gene.name, capture.only = TRUE,
                       min.ref.avgRPKM = 3, ref.avg.method = "median",
                       logR.cut = 1.5, font.cex = 0.6, heatmap.margin = c(5, 15), ...)

Arguments

data.name	an object of PatCNVData-class
sel.gene.name	a character vector containing gene names. A value of NULL instructs the function to select all the genes
capture.only	a logical value indicating if only captured exons should be used
min.ref.avgRPKM	minimum normalized exon-coverage threshold according to ref.avg.method
ref.avg.method	a character indicating if exon-level "median" or "mean" coverage information should be considered to filter out exons
logR.cut	only exon with absolute CNV values larger or equal to the threshold will be outputted
font.cex	expansion factor for font size
heatmap.margin	numeric vector of length 2 containing the margins (see par(mar= *)) for column and row names, respectively
...	additional arguments passed on to image

Author(s)

Chen Wang

See Also

plot CNV results of given chromosome plotChrCNV; plot autosome CNV results plotAutosomeCNV

Examples

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

#===  plot gene CNV heatmap
plotGeneHeatmap(sim.cnvData,
                       c("NAGA","ARFGAP3","CYB5R3","POLR3H","FAM109B"))

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