scanMultiCovg: Scan exome coverage of multiple samples

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

Description

This function summarizes exon-level coverage for multi samples defined by given patternCNV session information.

Usage

scanMultiCovg(session.name, sample.type = NULL, bin.size = 10, 
                     is.verbose = TRUE, is.plot = FALSE)

Arguments

session.name	an object of PatCNVSession-class, which is generated by createSession
sample.type	a character vector of sample type defined in sample information file: e.g. "Germline" or "Somatic". A value of NULL instructs the function to select all the samples regardless sample types
bin.size	numeric value of genomic bin-size for exons
is.verbose	logical value indicating if the progress information is printed
is.plot	logical value indicating if the coverage summary plot is generated

Value

This function returns an object of PatCNVData-class containing per-sample coverage information generated.

Author(s)

Chen Wang

See Also

createSession

Examples

#=== load a simulation example
config.filename <- "sim1.ini"
makeSimulation(config.filename)
sim.session <- createSession(config.filename)

#=== scan coverages of multiple samples
germline.data <- scanMultiCovg(session.name=sim.session)

#=== print BP-level coverage per sample
sampleCoverage(germline.data)

#=== print median/mean exon-coverage of selected genes
avgExonCoverage(germline.data,gene.name=c("BIK"))

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