ballgown (version 2.4.2)

annotate_assembly: 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

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.

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.

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)