readCoverageFile {PureCN} | R Documentation

## Read coverage file

### Description

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

### Usage

    readCoverageFile(file, format, zero = NULL, read.length = 100)

### Arguments

`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.

### Value

A `data.frame` with the parsed coverage information.

### Author(s)

Markus Riester

### See Also

`calculateBamCoverageByInterval`

### Examples

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

[Package PureCN version 1.10.0 Index]