scanSingleCovg: Scan exome coverage of single sample

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

Description

This function is not supposed to be directly called by users. Rather, it should be called by scanMultiCovg

Usage

scanSingleCovg(wig.filename, sample.ID, exon.bin.vec, is.capture.vec, 
                      is.plot = FALSE, log.for.plot = TRUE, plot.output.DIR, 
                      bin.size = 10, ylab = "# of exons", 
                      xlab = "log2(coverage per base)")

Arguments

wig.filename	the name of input WIG file
sample.ID	character name of input sample
exon.bin.vec	a numeric vector indicating number of genomic bins per exon
is.capture.vec	a logical vector indicating if corresponding is captured
is.plot	a logical value indicating if generating coverage plot
log.for.plot	a logical value indicating if the coverage plot is according to log-scale
plot.output.DIR	name of directory for generating plot
bin.size	genomic bin-size
xlab	a title for the x axis
ylab	a title for the y axis

Details

Not for users

Value

coverage information of a single sample

Author(s)

Chen Wang

See Also

scanMultiCovg

Examples

#=== locate an example wig file, which is average pattern of simulation data
wigfile <- system.file("extdata","avg_pattern.wig",package="patternCNV")

#=== load a simulation session with generated pattern files
config.filename <- 'sim2.ini'
makeSimulation(config.filename,with.pattern=TRUE)
sim.session <- createSession(config.filename)
is.capture <- exonInfo(sim.session,attri="is.captured")
exon.Nbin <- exonInfo(sim.session,attri="N.exon.bin")

#=== return coverage information from specificed wig file
wig.out <- scanSingleCovg(wigfile,"avg",exon.Nbin,is.capture)

#=== plot coverage versus position (Mb)
exon.startpos <- exonInfo(sim.session,attri="start")
plot(exon.startpos/1e6,wig.out,log="y",xlab="position (Mb)",ylab="BP-level coverage")

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