geneCoverageQC: Quality-check exon-coverage of given genes

Description Usage Arguments Author(s) See Also Examples

View source: R/geneCoverageQC.R

Description

This function displays coverage plot for given genes, to facilitate quality-check if samples having reasonable coverage in particular gene regions.

Usage

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geneCoverageQC(data.name, sel.gene.name, 
                      legend.layout = "topleft", legend.cex = 0.5)

Arguments

data.name

an object of PatCNVData-class

sel.gene.name

a character vector of genes of interest

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

legend.cex

legend character expansion factor relative to current par("cex")

Author(s)

Chen Wang

See Also

chrCoverageQC

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)

#=== generate coverage plot for two genes
geneCoverageQC(germline.data, c("BIK","TTLL1"))

#=== generate the same coverage plot but hiding sample-legend for clarity
geneCoverageQC(germline.data, c("BIK","TTLL1"), legend.layout="none")

hshdndx/new-to-CNV documentation built on May 16, 2017, 11:26 p.m.