get_exon_skipping_junction: Compute the resulting junction (junc_id) for exon skipping of...

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

Compute the resulting junction (junc_id) for exon skipping of given exon and transcript.

Description

Compute the resulting junction (junc_id) for exon skipping of given exon and transcript.

Usage

get_exon_skipping_junction(exon_id, exons, transcript_id, transcripts)

Arguments

exon_id	A vector of exon IDs
exons	A vector of the genomic coordinates of the exon.
transcript_id	A vector of transcript IDs
transcripts	a GRangesList with transcripts defined as GRanges of exons created by GenomicFeatures::exonsBy(txdb, by = c("tx"), use.names = TRUE).

Value

A list of junction IDs formatted as ⁠<chr>_<left>_<right>_<strand>⁠.

Examples

transcript_id <- c("ENST00000243347", "ENST00000460812")
exon_id <- c("ENSE00000840477", "ENSE00003481758")
exons <- c("chr2:152222570-152222731:+", "chr2:152226534-152226762:+")
transcripts <- toy_transcripts

get_exon_skipping_junction(exon_id, exons, transcript_id, transcripts)

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