coverageOnTarget {R453Plus1Toolbox} | R Documentation

## Computes the coverage restricted to the target region.

### Description

This method computes the approximate coverage of each base in a given region.

### Usage

    coverageOnTarget(alnReads, targetRegion)

### Arguments

`alnReads` | A list as returned by `scanBam` storing aligned reads.
`targetRegion` | The target region as a `GRanges` object. The chromosome names must fit to the chromosome names used in the alignment information of the given reads.

### Details

The detailed alignment information given by the CIGAR strings in .bam files are ignored by the function. Instead, it is assumed that the whole read alignes to the reference without indels. This is often not true for longer read (e.g. generated with Roche 454 Sequencing), but saves computation time.

### Value

A list of the same length as the `alnReads` argument. Each list element is an integer vector of the same length as the target region (in bases) and stores the coverage generated by the reads from the corresponding list element of `alnReads`.

### Author(s)

Hans-Ulrich Klein

### See Also

`scanBam`

### Examples

    library(Rsamtools)
    bamFile = system.file("extdata", "SVDetection", "bam", "N01.bam", package="R453Plus1Toolbox")
    bam = scanBam(bamFile)
    region = GRanges(IRanges(start=118307205, end=118395936), seqnames=11)
    cov = coverageOnTarget(bam, region)

[Package R453Plus1Toolbox version 1.28.1 Index]