EnrichResult-class

Class 'EnrichResult'
This class represents the result of enrich analysis

classes

To implement disease ontology (DO) enrichment analysis, this package is designed and presents
a double weighted model based on the latest annotations of the human genome with DO terms, by
integrating the DO graph topology on a global scale. This package exhibits high accuracy that
it can identify more specific DO terms, which alleviates the over enriched problem. The package
includes various statistical models and visualization schemes for discovering the associations
between genes and diseases from biological big data.

Haixiu Yang

EnrichDO

a Global Weighted Model for Disease Ontology Enrichment Analysis

Liang Cheng

Hongyu Fu

EnrichResult-class function

<dl>
<dt><code>enrich</code></dt>
<dd>a data frame of enrichment result</dd></dl>
<dt><code>test</code></dt>
<dd>Statistical test</dd>
<dt><code>method</code></dt>
<dd>Multiple test correction methods</dd>
<dt><code>m</code></dt>
<dd>the maximum number of ancestor layers for ontology enrichment</dd>
<dt><code>maxGsize</code></dt>
<dd>The maximum number of DOTerm genes in enrichment analysis</dd>
<dt><code>minGsize</code></dt>
<dd>The minimum number of DOTerm genes in enrichment analysis</dd>
<dt><code>traditional</code></dt>
<dd>Indicates whether the traditional ORA method is used</dd>
<dt><code>delta</code></dt>
<dd>The highest p-value of significance for each node</dd>
<dt><code>penalize</code></dt>
<dd>Whether to use penalty function in enrichment analysis</dd>
<dt><code>interestGenes</code></dt>
<dd>A valid interest gene set</dd>

Slots

Author

Class 'EnrichResult'
This class represents the result of enrich analysis — EnrichResult-class

<dl>
<dt><code>enrich</code></dt>
<dd>a data frame of enrichment result</dd>


<dt><code>test</code></dt>
<dd>Statistical test</dd>


<dt><code>method</code></dt>
<dd>Multiple test correction methods</dd>


<dt><code>m</code></dt>
<dd>the maximum number of ancestor layers for ontology enrichment</dd>


<dt><code>maxGsize</code></dt>
<dd>The maximum number of DOTerm genes in enrichment analysis</dd>


<dt><code>minGsize</code></dt>
<dd>The minimum number of DOTerm genes in enrichment analysis</dd>


<dt><code>traditional</code></dt>
<dd>Indicates whether the traditional ORA method is used</dd>


<dt><code>delta</code></dt>
<dd>The highest p-value of significance for each node</dd>


<dt><code>penalize</code></dt>
<dd>Whether to use penalty function in enrichment analysis</dd>


<dt><code>interestGenes</code></dt>
<dd>A valid interest gene set</dd>


</dl>

EnrichResult-class: Class 'EnrichResult' This class represents the result of enrich analysis

Description

Arguments

Slots

Author