pctOverlap {ballgown} | R Documentation

## 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

### 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).

### 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`.

### Author(s)

Alyssa Frazee

### 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%

[Package ballgown version 2.19.3 Index]