correctCoverageBias: Correct for library-specific coverage biases

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

Correct for library-specific coverage biases

Description

Takes as input coverage data and a mapping file for GC content and optionally replication timing. Will then normalize coverage data for GC-bias. Plots the pre and post normalization GC profiles.

Usage

correctCoverageBias(
  coverage.file,
  interval.file,
  output.file = NULL,
  plot.bias = FALSE,
  plot.max.density = 50000,
  output.qc.file = NULL
)

Arguments

coverage.file	Coverage file or coverage data parsed with the readCoverageFile function.
interval.file	File providing GC content for each exon in the coverage files. First column in format CHR:START-END. Additional optional columns provide gene symbols, mappability and replication timing. This file is generated with the preprocessIntervals function.
output.file	Optionally, write file with GC corrected coverage. Can be read with the readCoverageFile function.
plot.bias	Optionally, plot 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.bias parameter is set as FALSE, this will be ignored.
output.qc.file	Write miscellaneous coverage QC metrics to file.

Author(s)

Angad Singh, Markus Riester

See Also

preprocessIntervals

Examples

normal.coverage.file <- system.file("extdata", "example_normal.txt.gz",
    package = "PureCN")
interval.file <- system.file("extdata", "example_intervals.txt",
    package = "PureCN")
coverage <- correctCoverageBias(normal.coverage.file, interval.file)

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