chrCoverageQC: Quality-check exome coverage across chromosomes

Description Usage Arguments Author(s) See Also Examples

View source: R/chrCoverageQC.R

Description

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

Usage

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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

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#=== 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 16, 2017, 11:26 p.m.