collapseStrand: Collapse a 'MethPat' object by strand.

In PeteHaitch/MethylationTuples: Tools for analysing methylation patterns at genomic tuples

Description

A MethPat object may contain separate counts for the positive (+) and negative (-) strands. In some instances it may be desirable to collapse these observations across strands. This function will combine the loci and sum their associated counts. The co-ordinates of the collapsed loci will have the strand set to *, although positions will be with respect to the forward strand. For example, the CpG with co-ordinates chr1:10 on the + strand and chr1:11 on the - strand will be collapsed to chr1:10 with the strand set to *.

Usage

collapseStrand(methpat)

Arguments

methpat

A MethPat object.

Details

NOTE: Collapsing by strand is only possible if the methtype of the object is CG, since neither CHG nor CHH is a strand-symmetric motif.

NOTE: Any mcols of the methpat object will be dropped.

Value

An updated version of the MethPat object, where the loci and their associated counts have been combined across strands.

PeteHaitch/MethylationTuples documentation built on May 8, 2019, 1:30 a.m.