avgExonCoverage: Compute average coverage of exons across samples

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

Description

This function returns across-sample average coverage of all the exons or selected exons from given genes. The average calculation could be mean or median, while the later is default method considering its robustness towards outliers.

Usage

avgExonCoverage(obj, gene.name = NULL, type = c("RPKM"), method = "median")

Arguments

obj	an object of PatCNVData-class
gene.name	a character vector of gene.name. A value of NULL instructs the function to use all the genes
type	"RPKM" or "raw" coverage. Default value "RPKM" refers to normalized coverage
method	"mean" or "median"; it specificies how average coverage is computed

Value

a numerical vector of average coverages of exons

Author(s)

Chen Wang

See Also

sample-level coverage summary sampleCoverage

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 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.