PureCN (version 1.0.4)

poolCoverage: Pool coverage from multiple samples

Description

Averages the coverage of a list of samples.

Usage

poolCoverage(all.data, remove.chrs = c(), w = NULL)

Arguments

all.data

List of normals, read with readCoverageGatk.

remove.chrs

Remove these chromosomes from the pool.

w

List of weights for each sample

Value

Examples

gatk.normal.file <- system.file("extdata", "example_normal.txt", 
    package="PureCN")
gatk.normal2.file <- system.file("extdata", "example_normal2.txt", 
    package="PureCN")
gatk.normal.files <- c(gatk.normal.file, gatk.normal2.file)
gatk.tumor.file <- system.file("extdata", "example_tumor.txt", 
    package="PureCN")

normalDB <- createNormalDatabase(gatk.normal.files)

# get the best 2 normals and average them
gatk.best.normal.files <- findBestNormal(gatk.tumor.file, normalDB, 
    num.normals=2)
pool <- poolCoverage(lapply(gatk.best.normal.files, readCoverageGatk),
     remove.chrs=c('chrX', 'chrY'))