collapseDuplicatedReads-GAlignments-method: Collapse duplicated reads

In ORFik: Open Reading Frames in Genomics

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 'GAlignments'
collapseDuplicatedReads(x, addScoreColumn = TRUE)

Arguments

x	a GRanges, GAlignments or GAlignmentPairs object
addScoreColumn	= TRUE, if FALSE, only collapse and not add score column.

Value

a GRanges, GAlignments or GAlignmentPairs object, same as input

Examples

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

ORFik documentation built on March 27, 2021, 6 p.m.