predictExonsTerminal: Identify terminal exons

In ldg21/SGSeq: Splice event prediction and quantification from RNA-seq data

Description

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

Usage

predictExonsTerminal(candidates, frag_exonic, frag_intron, relCov, min_anchor,
  type = c("exon_L", "exon_R"), 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
min_anchor	Integer specifiying minimum anchor length
type	Character string indicating whether terminal exons should be identified to the left (“exon_L”) or right (“exon_R”) of provided splice sites
include_counts	Logical indicating whether counts of compatible fragments should be included in metadata column “N”
retain_coverage	Logical indicating whether coverage for each exon should be retained as an RleList in metadata column “coverage”. This allows filtering of features using more stringent criteria after the initial prediction.

Value

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

Author(s)

Leonard Goldstein

ldg21/SGSeq documentation built on Oct. 14, 2020, 9:51 p.m.