canonical_junctions: Build canonical junctions from transcripts

In TRON-Bioinformatics/splice2neo: Aberrant splice junction analysis with associated mutations

Build canonical junctions from transcripts

Description

Build canonical junctions from transcripts

Usage

canonical_junctions(tx)

Arguments

tx	a GRangesList of reference transcripts

Value

a character vector of canonical splice junction ids

We build all canonical splice junctions that are in the annotated input transcripts. The following lists implementation rules for adjacent canonical exon-exon junction:

• strand = +: e_i, s_{i+1}

• strand = -: e_{i+1}, s_{i}

We also include canonical intron-retention junctions. These are 5' donor or 3' acceptor sites of canonical exon-exon junctions that are not used in all isoforms of the gene. They are located within an exon of other transcripts. Canonical intron-retention junctions are defined by the coordinate of the last exon base and the next base. Therefore, we just need to check whether both bases are included in a single exon.

Examples

gtf_file <- system.file("extdata","GTF_files","Aedes_aegypti.partial.gtf",
  package="splice2neo")

tx <- parse_gtf(gtf_file)

canonical_junctions(tx[1:10])

TRON-Bioinformatics/splice2neo documentation built on July 27, 2024, 3:25 a.m.