exportCNVtable: Exports exon-level CNV information as per-sample tables

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

Description

This function outputs exon-level CNV information for each sample into a table, including basic exon information, raw and normalized coverage and CNV information.

Usage

exportCNVtable(session.name, data.name, 
                      output_suffix = "_CNV_table.txt", 
                      ref.avg.method = "median", min.ref.avgRPKM = 2, 
                      capture.only = TRUE, FDR.threshold = 0.05, 
                      logR.cut = 0.1, is.verbose = TRUE)

Arguments

session.name	an object of PatCNVSession-class
data.name	an object of PatCNVData-class
output_suffix	filename suffix of output sample tables
ref.avg.method	a character indicating if exon-level "median" or "mean" coverage information should be outputted in the table
min.ref.avgRPKM	minimum normalized coverage of output exons
capture.only	a logical value indicating if only captured exons should be outputted
FDR.threshold	only exon with FDR below the threshold will be outputted
logR.cut	only exon with absolute CNV values larger or equal to the threshold will be outputted
is.verbose	logical value indicating if the progress information is printed

Author(s)

Chen Wang

See Also

computeMultiCNV

Examples

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

#=== compute CNV and generate heatmap of selected genes
germline.data <- computeMultiCNV(sim.session)

#=== export per-sample CNV tables for exons with absolute CNV values larger or equal to 0.5
exportCNVtable(sim.session,germline.data,logR.cut=0.5)

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