predict_cassette_exon: Predict novel cassette exons

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

Description

Novel cassette exons are predicted from pairs of novel splice junctions (SJ) that are located within an annotated intron and share the start and end coordinates of the intron:

X---------X   annotated intron
x---x         novel splice junction
      x---x   novel splice junction
X---NNN---X  predicted cassette exon (N)

First, the novel SJs are filtered: Only SJs that are located within an annotated intron and that share their start or end coordinates with the intron are retained. All introns that share both their start and end with a novel SJ are tested for cassette exons. If the two novel SJs within an intron do not overlap and are on the same strand, a novel cassette exon is predicted.

Usage

predict_cassette_exon(sj_unann, introns)

Arguments

sj_unann	GRanges object with unannotated splice junctions.
introns	GRanges object. Intron annotations, e.g. the "introns" slot from the object returned by prepare_annotation().

Value

List with two slots: "ne" is a data.frame with the coordinates of the identifies cassette exons. It has 6 columns: seqnames, lend, start, end, rstart and strand. "sj" is a GRanges object with the SJs from the parameter sj_unann that were not used to predict cassette exons.

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