readCoverageFile {PureCN}R Documentation

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)

Arguments

file

Target coverage file.

format

File format. If missing, derived from the file extension. Currently only GATK DepthofCoverage and CNVkit formats supported.

zero

Start position is 0-based. Default is FALSE for GATK, TRUE for BED file based intervals.

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", 
    package="PureCN")
coverage <- readCoverageFile(tumor.coverage.file)


[Package PureCN version 1.8.1 Index]