predictExonsInternal

<code>IRanges</code> of candidate internal exons

candidates

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

frag_exonic

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

frag_intron

Minimum relative coverage required for exon prediction

relCov

Integer specifiying minimum anchor length

min_anchor

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

include_counts

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

retain_coverage


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


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.

predictExonsInternal: Identify internal exons

Description

Usage

Arguments

Value