SetBasedEnrichmentTest-class

SetBasedEnrichmentTest

run_test,SetBasedEnrichmentTest-method

PRIVATE class : An S4 class to represent a Hypergeometric tests in
mulea.

Traditional gene set enrichment analyses are typically limited to a
few ontologies and do not account for the interdependence of gene sets or
terms, resulting in overcorrected p-values. To address these challenges, we
introduce 'mulea', an R package offering comprehensive overrepresentation
and functional enrichment analysis. 'mulea' employs an innovative empirical
false discovery rate (eFDR) correction method, specifically designed for
interconnected biological data, to accurately identify significant terms
within diverse ontologies. Beyond conventional tools, 'mulea' incorporates a
wide range of ontologies encompassing Gene Ontology, pathways, regulatory
elements, genomic locations, and protein domains. This flexibility empowers
researchers to tailor enrichment analysis to their specific questions, such
as identifying enriched transcriptional regulators in gene expression data
or overrepresented protein domains in protein sets. To facilitate seamless
analysis, 'mulea' provides gene sets (in standardized GMT format) for 27
model organisms, covering 16 databases and various identifiers.
Additionally, the 'muleaData' ExperimentData Bioconductor package simplifies
access to these 879 pre-defined ontologies. Furthermore, 'mulea''s
architecture allows for easy integration of user-defined ontologies,
expanding its applicability across diverse research areas.

Tam<c3><a1>s Stirling

mulea

Enrichment Analysis using Multiple Ontologies and FDR Correction

Cezary Turek

Marton Olbei

Tamas Stirling

Gergely Fekete

Ervin Tasnadi

Leila Gul

Balazs Bohar

Balazs Papp

Wiktor Jurkowski

Eszter Ari

SetBasedEnrichmentTest-class function

<dl><dt>model</dt>
<dd>Object of s4 class represents mulea Test.</dd></dl>

Arguments

<ul>
<li><code>run_test(SetBasedEnrichmentTest)</code>: runs test calculations.</li>
</ul>

Methods (by generic)

<dl>
<dt><code>gmt</code></dt>
<dd>A data.frame representing GMT's representation of model.</dd></dl>
<dt><code>element_names</code></dt>
<dd>A data from experiment to analyse across model.</dd>
<dt><code>pool</code></dt>
<dd>A background data to count test.</dd>
<dt><code>nthreads</code></dt>
<dd>Number of processor's threads used in calculations.</dd>

Slots

PRIVATE class : An S4 class to represent a Hypergeometric tests in
mulea. — SetBasedEnrichmentTest-class

<dl>

<dt>model</dt>
<dd>Object of s4 class represents mulea Test.</dd>

</dl>

<dl>
<dt><code>gmt</code></dt>
<dd>A data.frame representing GMT's representation of model.</dd>


<dt><code>element_names</code></dt>
<dd>A data from experiment to analyse across model.</dd>


<dt><code>pool</code></dt>
<dd>A background data to count test.</dd>


<dt><code>nthreads</code></dt>
<dd>Number of processor's threads used in calculations.</dd>


</dl>

SetBasedEnrichmentTest-class: PRIVATE class : An S4 class to represent a Hypergeometric tests in mulea.

Description

Usage

Value

Arguments

Methods (by generic)

Slots