readCoverageFile: Read coverage file
In PureCN: Copy number calling and SNV classification using targeted short read sequencing

Read coverage file produced by external tools like The Genome Analysis Toolkit or by calculateBamCoverageByInterval.

1	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 `FALSE` for GATK, `TRUE` for BED file based intervals.
`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

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tumor.coverage.file <- system.file("extdata", "example_tumor.txt", 
    package="PureCN")
coverage <- readCoverageFile(tumor.coverage.file)

PureCN documentation built on Nov. 8, 2020, 5:37 p.m.

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