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

Description Usage Arguments Author(s) See Also Examples

View source: R/exportCNVtable.R

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

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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

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#=== 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 16, 2017, 11:26 p.m.