PureCN (version 1.0.3)

correctCoverageBias: Correct for GC bias

Description

Takes as input coverage data in GATK format (or data read by readCoverageGatk) and a mapping file for GC content, and then uses a loess normalization for bias correction. Largely follows the GC correction of the TitanCNA package.

Usage

correctCoverageBias(gatk.coverage.file, gc.gene.file, 
    output.file = NULL)

Arguments

gatk.coverage.file

Exon coverage file as produced by GATK. Either a file name or data parsed with the readCoverageGatk function.

gc.gene.file

File providing GC content for each exon in the coverage files. First column in format CHR:START-END. Second column GC content (0 to 1). Third column provides gene symbols, which are optional, but used in runAbsoluteCN to generate gene level calls.

output.file

Optionally, write minimal GATK coverage file with GC corrected coverage.

Value

• GC normalized coverage.

Examples

gatk.normal.file <- system.file("extdata", "example_normal.txt", 
    package="PureCN")
gc.gene.file <- system.file("extdata", "example_gc.gene.file.txt", 
    package="PureCN")
coverage <- correctCoverageBias(gatk.normal.file, gc.gene.file)

Run the code above in your browser using DataCamp Workspace