Compute the resulting junction (junc_id) for exon skipping of given exon and transcript. — get_exon_skipping_junction • splice2neo

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

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)
#> $ENST00000243347
#> [1] NA
#> 
#> $ENST00000460812
#> [1] NA
#>