enrichResult-class

plot,enrichResult-method

show,enrichResult-method

summary,enrichResult-method


Class "enrichResult"
This class represents the result of enrichment analysis.


classes

This package implements five methods proposed by
Resnik, Schlicker, Jiang, Lin and Wang respectively
for measuring semantic similarities among DO terms and
gene products. Enrichment analyses including hypergeometric
model and gene set enrichment analysis are also implemented
for discovering disease associations of high-throughput
biological data.

Guangchuang Yu

DOSE

Disease Ontology Semantic and Enrichment analysis

enrichResult-class function

 <dl>
<dt><code>result</code></dt><dd>enrichment analysis</dd> <dt><code>pvalueCutoff</code></dt><dd>pvalueCutoff</dd> <dt><code>pAdjustMethod</code></dt><dd>pvalue adjust method</dd> <dt><code>qvalueCutoff</code></dt><dd>qvalueCutoff</dd> <dt><code>organism</code></dt><dd>only "human" supported</dd> <dt><code>ontology</code></dt><dd>biological ontology</dd> <dt><code>gene</code></dt><dd>Gene IDs</dd> <dt><code>keytype</code></dt><dd>Gene ID type</dd> <dt><code>universe</code></dt><dd>background gene</dd> <dt><code>geneInCategory</code></dt><dd>gene and category association</dd> <dt><code>gene2Symbol</code></dt><dd>mapping gene to Symbol</dd> <dt><code>geneSets</code></dt><dd>gene sets</dd> <dt><code>readable</code></dt><dd>logical flag of gene ID in symbol or not.</dd> </dl>

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enrichResult-class: Class "enrichResult" This class represents the result of enrichment analysis.

Description

Arguments

Slots

See Also