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

In R453Plus1Toolbox: A package for importing and analyzing data from Roche's Genome Sequencer System

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

Value

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

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)
targetReads = readsOnTarget(bam, region)
sum(targetReads[[1]])

R453Plus1Toolbox documentation built on Nov. 8, 2020, 5:59 p.m.