SGSeq (version 1.2.2)

predictExonsInternal: Identify internal exons

Description

Identify internal exons based on candidate internal exons and compatible read coverage.

Usage

predictExonsInternal(candidates, frag_exonic, frag_intron, relCov, include_counts, retain_coverage)

Arguments

candidates

IRanges of candidate internal exons

frag_exonic

IRangesList with exonic regions from alignments

frag_intron

IRangesList with introns implied by spliced alignments

relCov

Minimum relative coverage required for exon prediction

include_counts

Logical indicating whether counts of compatible fragments should be included in elementMetadata column “N”

retain_coverage

Logical indicating whether coverages for each exon should be retained as an IntegerList in elementMetadata column “coverage”. This allows filtering of features using more stringent criteria after the initial prediction.

Value

IRanges of internal exons with elementMetadata column “type” and optionally “N” for include_counts = TRUE, “N_splicesite”, “coverage” for retain_coverage = TRUE