doterms

A dataset includes 4831 DO terms of hierarchical information, annotated gene information, and weight information

datasets

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

doterms function

A data frame with 4813 rows and 10 variables:<dl>
 <dt>DOID</dt>
<dd>the DOterm ID on enrichment</dd> <dt>level</dt>
<dd>the hierarchy of the DOterm in the DAG graph</dd> <dt>gene.arr</dt>
<dd>all genes related to the DOterm</dd> <dt>weight.arr</dt>
<dd>gene weights in each node</dd> <dt>parent.arr</dt>
<dd>the parent node of the DOterm</dd> <dt>parent.len</dt>
<dd>the number of parent.arr</dd> <dt>child.arr</dt>
<dd>child nodes of the DOterm</dd> <dt>child.len</dt>
<dd>the number of child.arr</dd> <dt>gene.len</dt>
<dd>the number of all genes related to the DOterm</dd> <dt>DOTerm</dt>
<dd>the standard name of the DOterm</dd>
</dl>

Format

Detailed annotation information for 4831 DO terms. — doterms

A data frame with 4813 rows and 10 variables:<dl>
 <dt>DOID</dt>
<dd>the DOterm ID on enrichment</dd>

 <dt>level</dt>
<dd>the hierarchy of the DOterm in the DAG graph</dd>

 <dt>gene.arr</dt>
<dd>all genes related to the DOterm</dd>

 <dt>weight.arr</dt>
<dd>gene weights in each node</dd>

 <dt>parent.arr</dt>
<dd>the parent node of the DOterm</dd>

 <dt>parent.len</dt>
<dd>the number of parent.arr</dd>

 <dt>child.arr</dt>
<dd>child nodes of the DOterm</dd>

 <dt>child.len</dt>
<dd>the number of child.arr</dd>

 <dt>gene.len</dt>
<dd>the number of all genes related to the DOterm</dd>

 <dt>DOTerm</dt>
<dd>the standard name of the DOterm</dd>


</dl>

doterms: Detailed annotation information for 4831 DO terms.

Description

Usage

Arguments

Format