correctCoverageBias {PureCN} | R Documentation |
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.
correctCoverageBias( coverage.file, interval.file, output.file = NULL, plot.bias = FALSE, plot.max.density = 50000, output.qc.file = NULL )
coverage.file |
Coverage file or coverage data parsed with the
|
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 |
output.file |
Optionally, write file with GC corrected coverage. Can be
read with the |
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 |
output.qc.file |
Write miscellaneous coverage QC metrics to file. |
Angad Singh, Markus Riester
normal.coverage.file <- system.file("extdata", "example_normal.txt", package="PureCN") interval.file <- system.file("extdata", "example_intervals.txt", package="PureCN") coverage <- correctCoverageBias(normal.coverage.file, interval.file)