correctCoverageBias {PureCN} | R Documentation

## Correct for GC bias

### Description

Takes as input coverage data and a mapping file for GC content. Will then normalize coverage data for GC-bias. Optionally plots the pre and post normalization GC profiles.

### Usage

    correctCoverageBias(coverage.file, gc.gene.file, output.file = NULL,
      method = c("LOESS", "POLYNOMIAL"), plot.gc.bias = FALSE,
      plot.max.density = 50000)

### Arguments

`coverage.file` | Coverage file or coverage data parsed with the `readCoverageFile` 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. This file can be generated with GATK GCContentByInterval tool or with the `calculateGCContentByInterval` function.
`output.file` | Optionally, write file with GC corrected coverage. Can be read with the `readCoverageFile` function.
`method` | Two options for normalization are available: The default "LOESS" largely follows the GC correction of the TitanCNA package. The "POLYNOMIAL" method models the coverage data as a polynomial of degree three and normalizes using the EM approach. The "POLYNOMIAL" is expected to be more robust for very small targeted panels. "POLYNOMIAL" does not support off-target reads.
`plot.gc.bias` | Optionally, plot GC profiles of the pre-normalized and post-normalized coverage. Provides a quick visual check of coverage bias.
`plot.max.density` | By default, if the number of intervals in the probe-set is > 50000, uses a kernel density estimate to plot the coverage distribution. This uses the `stat_density` function from the ggplot2 package. Using this parameter, change the threshold at which density estimation is applied. If the `plot.gc.bias` parameter is set as `FALSE`, this will be ignored.

### Author(s)

Angad Singh, Markus Riester

### See Also

`calculateGCContentByInterval`

### Examples

    normal.coverage.file <- system.file("extdata", "example_normal.txt",
        package="PureCN")
    gc.gene.file <- system.file("extdata", "example_gc.gene.file.txt",
        package="PureCN")
    # normalize using default LOESS method
    coverage <- correctCoverageBias(normal.coverage.file, gc.gene.file)
    # normalize with POLYNOMIAL method for small panels
    coverage <- correctCoverageBias(normal.coverage.file, gc.gene.file,
        method="POLYNOMIAL", plot.gc.bias=TRUE)

[Package PureCN version 1.8.1 Index]