sj_touching_exon: Determine which side of the splice junction touches an exon

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

Description

Find all exons with the same strand as the splice junction and that touch it. If a sj touches two exons, the exons must come from the same gene.

Usage

sj_touching_exon(seqnames, start, end, strand, exons)

Arguments

seqnames	Character string or factor. Seqnames (chromosome) of the splice junction.
start	Integer scalar. Start of the splice junction.
end	Integer scalar. End of the splice junction.
strand	Character string or factor. Strand of the splice junction ("-" or "+").
exons	GRanges object. Annotated exons.

Value

A string that defines which side of the splice junction is touching an exon: "both", "start", "end", NA if the splice junction does not touch an exon or if the exons come from different genes.

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