computeMultiCNV: Compute copy number variation (CNV) for multiple samples

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

Description

This function returns an object of PatCNVData-class.

Usage

computeMultiCNV(session.name, data.name = NULL, sample.type = NULL,
                       ref.type = "average.pattern", episl = 1, 
                       small.delta = 1e-05, bin.size = 10, 
                       zero.median.adjust = TRUE, is.verbose = FALSE)

Arguments

session.name	an object of PatCNVSession-class
data.name	an object of PatCNVData-class. A NULL value instructs the function to create a new PatCNVData-class object
sample.type	a character vector containing sample types. A value of NULL instructs the function to select all the types
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
zero.median.adjust	logical value indicating if computed CNV should be adjusted to have zero median
is.verbose	logical value indicating if the progress information is printed

Value

an object of PatCNVSession-class, with CNV log2-ratio computed

Author(s)

Chen Wang

See Also

Scan exome coverage of multiple samples scanMultiCovg

Examples

#==========================================================
#=== 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.