Computes the coverage restricted to the target region.

Description

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

Usage

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coverageOnTarget(alnReads, targetRegion)

Arguments

alnReads

A list as returned by scanBam storing aligned reads.

targetRegion

The target region as a RangesList. 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

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

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