analyzeVariants

object

If more than <code>maxnvariant</code> variants are
identified in an event, the event is skipped, resulting in a warning.
Set to <code>NA</code> to include all events.

maxnvariant

Character string indicating whether identified splice
variants should be filtered. Possible options are <dquote>default</dquote>
(only include variants for events with all variants closed),
<dquote>closed</dquote> (only include closed variants) and <dquote>all</dquote>
(include all variants).

include

Integer specifying minimum denominator when
calculating variant frequencies. The total number of boundary-spanning
reads must be equal to or greater than <code>min_denominator</code> for at
least one event boundary. Otherwise estimates are set to <code>NA</code>.
If <code>NA</code>, all estimates are returned.

min_denominator

Integer specifiying minimum anchor length

min_anchor

Number of cores available for parallel processing

cores

High-level function for the analysis of splice variants from
splice graph features. Splice variants are identified with
<code><a href="/link/findSGVariants?package=SGSeq&version=1.6.2" rd-options="" data-mini-rdoc="SGSeq::findSGVariants">findSGVariants</a></code>. Representative counts are obtained
and variant frequencies estimated with <code><a href="/link/getSGVariantCounts?package=SGSeq&version=1.6.2" rd-options="" data-mini-rdoc="SGSeq::getSGVariantCounts">getSGVariantCounts</a></code>.

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

analyzeVariants function

Character string indicating whether identified splice
variants should be filtered. Possible options are <dQuote>default</dQuote>
(only include variants for events with all variants closed),
<dQuote>closed</dQuote> (only include closed variants) and <dQuote>all</dQuote>
(include all variants).

High-level function for the analysis of splice variants from
splice graph features. Splice variants are identified with
<code><a href="findSGVariants" rd-options="">findSGVariants</a></code>. Representative counts are obtained
and variant frequencies estimated with <code><a href="getSGVariantCounts" rd-options="">getSGVariantCounts</a></code>.

analyzeVariants: Analysis of splice variants

Description

Usage

Arguments

Value

Examples