predictJunctions

<code>IRangesList</code> with exonic regions from alignments

frag_exonic

<code>IRangesList</code> with introns implied by spliced
alignments

frag_intron

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

min_junction_count

Minimum splice frequency required for a splice junction
to be included

Integer specifiying minimum anchor length

min_anchor

Logical indicating whether coverage for each
exon should be retained as an <code>RleList</code> in metadata
column <dquote>coverage</dquote>. This allows filtering of features
using more stringent criteria after the initial prediction.

retain_coverage

Identify splice junctions from genomic RNA-seq read alignments.

internal

SGSeq is a software package for analyzing splice events from
	     RNA-seq data. Input data are sequence reads mapped to a reference
	     genome in BAM format. Genes are represented as a genome-wide
	     splice graph, which can be obtained from existing annotation or
	     can be predicted from the data. Splice events are identified
	     from the graph and are quantified locally using structurally
	     compatible reads at the start or end of each splice variant.
	     The package includes functions for splice event prediction,
	     quantification, visualization and interpretation.

Leonard Goldstein

SGSeq

Splice event prediction and quantification from RNA-seq data

predictJunctions function

Logical indicating whether coverage for each
exon should be retained as an <code>RleList</code> in metadata
column <dQuote>coverage</dQuote>. This allows filtering of features
using more stringent criteria after the initial prediction.

predictJunctions: Identify splice junctions

Description

Usage

Arguments

Value