pctOverlap {ballgown} | R Documentation |
calculate percent overlap between two GRanges objects
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%