ballgown (version 2.4.2)

pctOverlap: calculate percent overlap between two GRanges objects

Description

calculate percent overlap between two GRanges objects

Usage

pctOverlap(tx1, tx2)

Arguments

tx1

GRanges object

tx2

GRanges object

Value

percent overlap between tx1 and tx2, as defined by the ratio of the intersection of tx1 and tx2 to the union of tx1 and tx2.

Details

In the ballgown context, tx1 and tx2 are two transcripts, each represented by GRanges objects whose ranges represent the exons comprising the transcripts. The percent overlap is the number of nucleotides falling within both transcripts divided by the number of nucleotides falling within either transcript. Useful as a measure of transcript closeness (as it is essentially Jaccard distance).

Examples

data(bg)
gtfPath = system.file('extdata', 'annot.gtf.gz', package='ballgown')
annot_grl = gffReadGR(gtfPath, splitByTranscript=TRUE)
pctOverlap(structure(bg)$trans[[2]], annot_grl[[369]]) #79.9%