annotate_assembly: match assembled transcripts to annotated transcripts

Description Usage Arguments Details Value Author(s) Examples

View source: R/annotate_assembly.R

Description

match assembled transcripts to annotated transcripts

Usage

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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

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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 11, 2017, 12:12 a.m.