readCoverageFile: Read coverage file

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

Read coverage file

Description

Read coverage file produced by external tools like The Genome Analysis Toolkit or by calculateBamCoverageByInterval.

Usage

readCoverageFile(file, format, zero = NULL, read.length = 100)

Arguments

file	Target coverage file.
format	File format. If missing, derived from the file extension. Currently GATK3 DepthofCoverage, GATK4 CollectFragmentCounts (hdf5), and CNVkit formats supported.
zero	Start position is 0-based. Default is FALSE for GATK, TRUE for BED file based intervals.
read.length	For output formats which do not provide both counts and total coverages, approximate them using the specified read length.

Value

A data.frame with the parsed coverage information.

Author(s)

Markus Riester

See Also

calculateBamCoverageByInterval

Examples

tumor.coverage.file <- system.file("extdata", "example_tumor.txt.gz", 
    package = "PureCN")
coverage <- readCoverageFile(tumor.coverage.file)

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