which_exon_terminal: Determine terminal end of a splice junction

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

Description

This function computes if a splice junction (SJ) splices to a terminal exons. If the exon at the start of the SJ is terminal, the function returns "start", "end" if it is the exon at the end and "NA" if none of the exons are terminal.

Usage

which_exon_terminal(j, txdb = txdb, gtxdb = gtxdb, ebyTr = ebyTr)

Arguments

j	GRanges object. Novel splice junction.
txdb	TxDb object, e.g. the "txdb" slot from the prepare_annotation() return object.
gtxdb	GRanges object. All genes from the txdb parameter, e.g. obtained with GenomicFeatures::genes(txdb).
ebyTr	GRangesList object. All exons per transcript of the txdb parameter, e.g. obtained with GenomicFeatures::exonsBy(txdb, by = "tx", use.names = TRUE).

Value

Character string; either "start", "end" or "NA".

Details

The function first overlaps the SJ with all genes and then with all transcripts of the overlapping gene.

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