sampleCoverage: Summarize sample coverage

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

Description

This function gets total coverage of samples from an object of PatCNVData-class

Usage

sampleCoverage(obj, sample.type = NULL)

Arguments

obj	an object of PatCNVSession-class or PatCNVData-class
sample.type	a character vector containing sample types. A value of NULL instructs the function to select all the types of samples

Value

a numerical vector of total coverage per sample

Author(s)

Chen Wang

See Also

compute exon average coverage avgExonCoverage

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)

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