pctOverlap: calculate percent overlap between two GRanges objects
In ballgown: Flexible, isoform-level differential expression analysis

Description Usage Arguments Details Value Author(s) Examples

calculate percent overlap between two GRanges objects

1	pctOverlap(tx1, tx2)

`tx1`	GRanges object
`tx2`	GRanges object

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).

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.

Alyssa Frazee

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%