makeSimulation: Make patternCNV simulation files for easy testing

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

Description

This function is designed to faciliate users to test patternCNV, with generated WIG and/or pattern files.

Usage

makeSimulation(ini.file = "simu.ini",
                      sample.info.file = "sample_info.txt",
                      with.pattern = FALSE)

Arguments

ini.file	name of patternCNV configuration file, which is usually loaded by createSession
sample.info.file	name of sample information file which records sample name/type and path to sample WIG file
with.pattern	logical, whether trained pattern files need to be included in configuration file

Details

With succesful run of this function, the user should be able to automatically generate a configuration file and a sample information file under current working directory. The with.pattern option instructs whether generated configuration file includes already trained pattern files for simulation study.

Author(s)

Chen Wang

See Also

createSession

Examples

#=============================================================
#=== load a simulation example without generated pattern files
#=============================================================
config.filename <- "sim1.ini"
makeSimulation(config.filename)
sim.session <- createSession(config.filename)

#=== print session information
summary(sim.session)


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

#=== print session information
summary(sim.session)

#=== compute CNV and generate heatmap of selected genes
germline.data <- computeMultiCNV(sim.session)
plotGeneHeatmap(data.name=germline.data,
                       sel.gene.name=c("NAGA","ARFGAP3","CYB5R3","POLR3H","FAM109B"))

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