readsOnTarget: Check for each read whether it aligns within the given region.

Description

This methods checks (approximately) whether the given reads align within a given region.

Usage

readsOnTarget(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.

Value

The logical vector indicates for each read whether it overlaps with at least one base from any target region or not.

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. Hence, this method is useful to approximate the number of reads that align in the target region of a targeted sequencing experiment.

Examples

Run this code

library(Rsamtools)
bamFile = system.file("extdata", "SVDetection", "bam", "N01.bam", package="R453Plus1Toolbox")
bam = scanBam(bamFile)
region = RangesList("11"=IRanges(start=118307205, end=118395936))
targetReads = readsOnTarget(bam, region)
sum(targetReads[[1]])

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