annotate_assembly: match assembled transcripts to annotated transcripts

In alyssafrazee/ballgown-release: Flexible, isoform-level differential expression analysis

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)

alyssafrazee/ballgown-release documentation built on May 12, 2019, 1:40 a.m.