filter_terminal_sj: Filter novel exon predictions of potential terminal exon

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

Description

The exon predictions based on reads at the start or end of the novel splice junction are filtered and in case there are no reads with two splice junctions (one of the coordinates is NA), determine if the novel exon could be terminal. If yes, take the exon predictions from the corresponding end of the splice junction.

Usage

filter_terminal_sj(
  start_coords,
  end_coords,
  j,
  txdb = txdb,
  gtxdb = gtxdb,
  ebyTr = ebyTr
)

Arguments

start_coords	data.frame with exon predictions at the start of the novel SJ.
end_coords	data.frame with exon predictions at the end of the novel SJ.
j	data.frame with one row: the 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

data.frame with exon predictions, NULL if ambiguous or there are no supporting reads

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