readsToStartOrEnd {RiboProfiling}R Documentation

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

Description

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

Usage

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

#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")

[Package RiboProfiling version 1.23.0 Index]