geneCoverageQC: Quality-check exon-coverage of given genes

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 given genes, to facilitate quality-check if samples having reasonable coverage in particular gene regions.

Usage

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

#=== 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 17, 2019, 5:55 p.m.