poolCoverage: Pool coverage from multiple samples

In lima1/PureCN: Copy number calling and SNV classification using targeted short read sequencing

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.gz",
    package = "PureCN")
normal2.coverage.file <- system.file("extdata", "example_normal2.txt.gz",
    package = "PureCN")
normal.coverage.files <- c(normal.coverage.file, normal2.coverage.file)
pool <- poolCoverage(lapply(normal.coverage.files, readCoverageFile),
     remove.chrs = c("chrX", "chrY"))

lima1/PureCN documentation built on Sept. 17, 2024, 5:48 a.m.