predictExonsTerminal: Identify terminal exons

Description Usage Arguments Value Author(s)

View source: R/features-prediction.R

Description

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

Usage

1
2
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


Bioconductor-mirror/SGSeq documentation built on June 23, 2017, 4:25 p.m.