annotate_assembly {ballgown} | R Documentation

## match assembled transcripts to annotated transcripts

### Description

match assembled transcripts to annotated transcripts

### Usage

    annotate_assembly(assembled, annotated)

### Arguments

`assembled` | `GRangesList` object representing assembled transcripts
`annotated` | `GRangesList` object representing annotated transcripts

### Details

If `gown` is a `ballgown` object, `assembled` can be `structure(gown)$trans` (or any subset). You can generate a `GRangesList` object containing annotated transcripts from a gtf file using the `gffReadGR` function and setting `splitByTranscripts=TRUE`.

### Value

data frame, where each row contains `assembledInd` and `annotatedInd` (indexes of overlapping transcripts in `assembled` and `annotated`), and the percent overlap between the two transcripts.

### Author(s)

Alyssa Frazee

### Examples

    data(bg)
    gtfPath = system.file('extdata', 'annot.gtf.gz', package='ballgown')
    annot = gffReadGR(gtfPath, splitByTranscript=TRUE)
    info = annotate_assembly(assembled=structure(bg)$trans, annotated=annot)

[Package ballgown version 2.12.0 Index]