PureCN (version 1.0.3)

readCoverageGatk: Read GATK coverage files

Description

Read coverage file produced by The Genome Analysis Toolkit. The three only important columns in the GATK-generated file are: Target, total_coverage, and average_coverage.

Usage

readCoverageGatk(file)

Arguments

file

Exon coverage file as produced by GATK.

Value

• A data.frame with the parsed coverage information.

Examples

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