chrCoverageQC: Quality-check exome coverage across chromosomes

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

Description

This function displays coverage plot for chromosome 1-22, to facilitate quality-check.

Usage

chrCoverageQC(data.name, legend.layout = "topright", 
                     plot.cex = 2, legend.cex = 1)

Arguments

data.name	an object of PatCNVData-class
legend.layout	a character vector of legend location. It should be "bottomright", "bottom", "bottomleft", "left", "topleft", "top", "topright", "right", "center" or "none". When "none" is used, no legend will be plotted for clarity
plot.cex	plot point expansion factor
legend.cex	legend character expansion factor relative to current par("cex")

Author(s)

Chen Wang

See Also

exon-level QC: geneCoverageQC

Examples

 
#=== load a simulation example
config.filename <- 'sim1.ini'
makeSimulation(config.filename)
sim.session <- createSession(config.filename)

#=== scan coverages of multiple samples
germline.data <- scanMultiCovg(session.name=sim.session)

#=== only chr22 is supposed to have coverage
chrCoverageQC(data.name=germline.data,legend.layout='topleft')

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