Reads in GAlignments converted to either Read Start (5') or End (3') Positions

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Description

Reads in GAlignments converted to either Read Start (5') or End (3') Positions

Usage

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readsToStartOrEnd(aln, what)

Arguments

aln

A GAlignments object of the BAM mapping file.

what

A character object. Either "start" (the default) or "end" for read start or read end.

Value

A GRanges object containing either the read start or end genomic positions.

Examples

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#read the BAM file into a GAlignments object using
#GenomicAlignments::readGAlignments
#the GAlignments object should be similar to ctrlGAlignments object
data(ctrlGAlignments)
aln <- ctrlGAlignments
#transform the GAlignments object into a GRanges object (faster processing)
alnGRanges <- readsToStartOrEnd(aln, what = "end")