readCoverageFile {PureCN} | R Documentation |
Read coverage file produced by external tools like The Genome Analysis
Toolkit or by calculateBamCoverageByInterval
.
readCoverageFile(file, format, zero = NULL, read.length = 100)
file |
Target coverage file. |
format |
File format. If missing, derived from the file extension. Currently GATK3 DepthofCoverage, GATK4 CollectFragmentCounts (hdf5), and CNVkit formats supported. |
zero |
Start position is 0-based. Default is |
read.length |
For output formats which do not provide both counts and total coverages, approximate them using the specified read length. |
A data.frame
with the parsed coverage information.
Markus Riester
calculateBamCoverageByInterval
tumor.coverage.file <- system.file("extdata", "example_tumor.txt", package="PureCN") coverage <- readCoverageFile(tumor.coverage.file)