collapseDuplicatedReads-GAlignmentPairs-method: Collapse duplicated reads

In JokingHero/ORFik: Open Reading Frames in Genomics

Collapse duplicated reads

Description

For every GRanges, GAlignments read, with the same: seqname, start, (cigar) / width and strand, collapse and give a new meta column called "score", which contains the number of duplicates of that read. If score column already exists, will return input object!

Usage

## S4 method for signature 'GAlignmentPairs'
collapseDuplicatedReads(x, addScoreColumn = TRUE)

Arguments

x	a GRanges, GAlignments or GAlignmentPairs object
addScoreColumn	logical, default: (TRUE), if FALSE, only collapse and not keep score column of counts for collapsed reads. Returns directly without collapsing if reuse.score.column is FALSE and score is already defined.

Value

a GRanges, GAlignments, GAlignmentPairs or data.table object, same as input

Examples

gr <- rep(GRanges("chr1", 1:10,"+"), 2)
collapseDuplicatedReads(gr)

JokingHero/ORFik documentation built on April 7, 2024, 2:59 a.m.