predictJunctions: Identify splice junctions

Description Usage Arguments Value Author(s)

View source: R/features-prediction.R

Description

Identify splice junctions from genomic RNA-seq read alignments.

Usage

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predictJunctions(frag_exonic, frag_intron, min_junction_count, psi, min_anchor,
  retain_coverage)

Arguments

frag_exonic

IRangesList with exonic regions from alignments

frag_intron

IRangesList with introns implied by spliced alignments

min_junction_count

Minimum fragment count required for a splice junction to be included. If specified, argument alpha is ignored.

psi

Minimum splice frequency required for a splice junction to be included

min_anchor

Integer specifiying minimum anchor length

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 splice junctions with metadata columns “type” and “N”, and optionally “N_splicesite” for retain_coverage = TRUE

Author(s)

Leonard Goldstein


ldg21/SGSeq documentation built on May 7, 2019, 9:37 a.m.