computeSingleCNV: Compute copy number variation (CNV) for single sample

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

Description

This internal function computes copy number variation (CNV) for single sample. Not intended for users

Usage

computeSingleCNV(session.name, sample.name, ref.type = "average.pattern",
                        episl = 1, small.delta = 1e-05, bin.size = 10, 
                        is.verbose = TRUE)

Arguments

session.name	an object of PatCNVSession-class
sample.name	a character vector of sample name defined in sample information file
ref.type	"average.pattern" or "basic.paired". "average.pattern" instructs function make CNV calls using trained pattern files. "basic.paired" instructs function make CNV calls using paired normal/Germline sample.
episl	a small value adding to coverage to avoid doing log-transform on zero
small.delta	a small value
bin.size	numeric value of exon-level bin-size
is.verbose	logical value indicating if the progress information is printed

Details

Not for users

Value

numeric CNV log2-ratio value of single sample

Author(s)

Chen Wang

See Also

User should directly call computeMultiCNV

Examples

#==========================================================
#=== load a simulation example with generated pattern files
#==========================================================
config.filename <- 'sim2.ini'
makeSimulation(config.filename,with.pattern=TRUE)
sim.session <- createSession(config.filename)

#=== compute CNV of sample "c1"
c1.cnv <- computeSingleCNV(sim.session,"c1")

#=== plot CNV versus position (Mb)
exon.startpos <- exonInfo(sim.session,attri="start")
plot(exon.startpos/1e6, c1.cnv$CNV,
    xlab="position (Mb)",ylab="CNV log2ratio")

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