SGVariantCounts

<code>RangedSummarizedExperiment</code> with <code>SGVariants</code>
as <code>rowRanges</code> and assays <dquote>variantFreq</dquote>,
<dquote>countsVariant5p</dquote>, <dquote>countsVariant3p</dquote>,
<dquote>countsEvent5p</dquote>, <dquote>countsEvent3p</dquote>, and
optionally <dquote>countsVariant5pOr3p</dquote>

Creates an instance of S4 class <code>SGVariantCounts</code> for storing
splice variant counts.

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

SGVariantCounts function

<code>RangedSummarizedExperiment</code> with <code>SGVariants</code>
as <code>rowRanges</code> and assays <dQuote>variantFreq</dQuote>,
<dQuote>countsVariant5p</dQuote>, <dQuote>countsVariant3p</dQuote>,
<dQuote>countsEvent5p</dQuote>, <dQuote>countsEvent3p</dQuote>, and
optionally <dQuote>countsVariant5pOr3p</dQuote>

SGVariantCounts: Splice graph variant counts

Description

Usage

Arguments

Value

Examples