segmentCNV: Output CNV segmentation results

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

Description

This function outputs CNV segmentation results as .bed files and PDF files. It calls CBS segmentation method in DNAcopy

Usage

segmentCNV(session.name, data.name, output_suffix = "CNV_seg",
                  ref.avg.method = "median", min.ref.avgRPKM = 2, 
                  capture.only = TRUE, is.plot = TRUE, 
                  ylim = c(-3, 3), cex = 0.6, ...)

Arguments

session.name	an object of PatCNVSession-class
data.name	an object of PatCNVData-class
output_suffix	filename suffix of output CNV segmentation results
ref.avg.method	a character indicating if exon-level "median" or "mean" coverage information should be considered to filter out exons
min.ref.avgRPKM	minimum normalized exon-coverage threshold according to ref.avg.method
capture.only	a logical value indicating if only captured exons should be used
is.plot	a logical value indicating if CNV segmentation plots need to be generated
ylim	the y limits of the plot
cex	plot expansion factor relative to current par("cex")
...	other graphical parameters (see par)

Author(s)

Chen Wang

Examples

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

#=== compute CNV 
germline.data <- computeMultiCNV(sim.session)

#=== generate CNV segmentation results
segmentCNV( sim.session, germline.data)

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