extendTranscriptsPerGene: Extend truncated transcripts to the longest annotated...

In kauralasoo/txrevise: Extend and revise transcript annotatons.

Extend truncated transcripts to the longest annotated transcript.

Description

Identify transcripts that are flagged as start or end not found and extend them by adding missing exons from the longest transcript of the gene. Importantly, if the last exon at the truncated end is not present in the longest transcript, then the truncated transcript will not be extended, because there is no information supporting that exon junction.

Usage

extendTranscriptsPerGene(metadata, exons, cdss)

Arguments

metadata	data frame of transcript metadata (required columns: ensembl_transcript_id, longest_start, longest_end, cds_start_NF, cds_end_NF, cds_start_end_NF).
exons	named list of GRanges objects containing the exon coordinates for each transcript.
cdss	named list of GRanges objects containing the CDS coordinates for each transcript.

Value

List of GRanges lists (exons and cdss). Contains the update exon and CDS coordinates for transcripts that were previously truncated.

Author(s)

Kaur Alasoo

kauralasoo/txrevise documentation built on March 31, 2022, 12:03 p.m.