create_tr_entry: Create a new GTF entry for a novel terminal exon

In khembach/DISCERNS: DISCovery of unannotated Exons from RNa-seq Splice junction reads

Description

This function creates new GTF entries for a novel terminal exon and all transcripts in which it is located. As input, the function takes a list of transcript IDs and the GTF annotations of all exons from the transcripts. A random exon from each transcript is copied and the start and end coordinates are exchanged with those of the novel exon. The ranges of each transcript are adjusted to include the novel exon. The exon_number and exon_version are set to NA. The new exon_id, transcript_id and transcript_name are the original values with a suffix that identifies the novel exon by its ID: e.g. exon_id_ID or transcript_name_ID.

Usage

create_tr_entry(start, end, pred_id, tr_ids, exon_copy, tran)

Arguments

start	Integer scalar. Start of the novel exon.
end	Integer scalar. End of the novel exon.
pred_id	Integer scalar. ID of the predicted exon.
tr_ids	Character vector. Transcript IDs of all transcripts that contain the novel exon.
exon_copy	GRanges object. All exons from the transcripts that contain the novel exon.
tran	GRanges object with all transcript annotations from the organism.

Value

GRanges object with the exon and transcript annotation entries of the novel exon and all exons from the transcripts in tr_ids.

khembach/DISCERNS documentation built on June 23, 2020, 3:35 p.m.