predictSpliced

<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

Minimum relative coverage required for an internal exon
to be included

beta

Minimum relative coverage required for a terminal exon
to be included

gamma

Logical indicating whether counts of
compatible fragments should be included in elementMetadata column
&#147;N&#148;

include_counts

Logical indicating whether coverages for each
exon should be retained as an <code>IntegerList</code> in elementMetadata
column &#147;coverage&#148;. This allows filtering of features
using more stringent criteria after the initial prediction.

retain_coverage

Logical indicating whether predictions
should be limited to identification of splice junctions only

junctions_only


<code>IRanges</code>-based identification of splice junctions and exons


internal

RNA-seq data are informative for the analysis of known and
novel transcript isoforms. While the short length of RNA-seq
reads limits the ability to predict and quantify full-length
transcripts, short read data are well suited for the analysis
of individual alternative transcripts events (e.g. inclusion
or skipping of a cassette exon). The SGSeq package enables the
prediction, quantification and visualization of alternative
transcript events from BAM files.

predictSpliced: `IRanges`-based identification of splice junctions and exons

Description

Usage

Arguments

Value