correctCoverageBias {PureCN} | R Documentation |
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.
correctCoverageBias(coverage.file, gc.gene.file, output.file = NULL, method = c("LOESS", "POLYNOMIAL"), plot.gc.bias = FALSE, plot.max.density = 50000)
coverage.file |
Coverage file or coverage data parsed with the
|
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
|
output.file |
Optionally, write file with GC corrected coverage. Can be
read with the |
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 |
Angad Singh, Markus Riester
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)