poolCoverage {PureCN}R Documentation

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 readCoverageFile.

remove.chrs

Remove these chromosomes from the pool.

w

numeric(length(all.data)) vector of weights. If NULL, weight all samples equally.

Value

A data.frame with the averaged coverage over all normals.

Author(s)

Markus Riester

See Also

readCoverageFile

Examples


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

normalDB <- createNormalDatabase(normal.coverage.files)

# get the best 2 normals and average them
best.normal.coverage.files <- findBestNormal(tumor.coverage.file, normalDB, 
    num.normals=2)
pool <- poolCoverage(lapply(best.normal.coverage.files, readCoverageFile),
     remove.chrs=c("chrX", "chrY"))
[Package PureCN version 1.8.1 Index]