new_internal_transcript: Create new GTF annotation for a novel internal exon

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

Description

Given a novel exon, the function identifies the IDs of all transcripts that contain the upstream and downstream neighbouring exons (exon end is lend and exon start is rstart) of the novel exon. Each of the transcripts is copied and an entry for the the novel exon is created. 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

new_internal_transcript(
  seqn,
  lend,
  start,
  end,
  rstart,
  strand,
  pred_id,
  exons,
  tran
)

Arguments

seqn	Character string or factor. seqname of the novel exon.
lend	Integer scalar. End of the upstream exon.
start	Integer scalar. Start of the novel exon.
end	Integer scalar. End of the novel exon.
rstart	Integer scalar. Start of the downstream exon.
strand	Character string or factor. Strand of the novel exon (either "+" or "-").
pred_id	Integer scalar. ID of the novel exon.
exons	GRanges object. Exon annotations from a GTF file.
tran	GRanges object. Transcript annotations from a GTF file.

Value

GRanges object with GTF annotations of the novel exon and all its transcripts

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