get_ontological_gene_sets

Create list of gene sets defined by ontological annotation

R-interface to C++ implementation of the rank/score permutation based GSEA test (Subramanian et al 2005 <doi: 10.1073/pnas.0506580102>).

Daniel Greene

gsEasy

Gene Set Enrichment Analysis in R

get_ontological_gene_sets function

<dl><dt>ontology</dt>
<dd><code>ontology_index</code> object.</dd>
<dt>gene</dt>
<dd>Character vector of genes.</dd>
<dt>term</dt>
<dd>Character vector of term IDs annotated to corresponding genes.</dd>
<dt>min_genes</dt>
<dd>Minimum number of genes in gene sets.</dd>
<dt>max_genes</dt>
<dd>Maximum number of genes in gene sets.</dd></dl>

Arguments

Create list of gene sets defined by ontological annotation — get_ontological_gene_sets

<dl>

<dt>ontology</dt>
<dd><code>ontology_index</code> object.</dd>


<dt>gene</dt>
<dd>Character vector of genes.</dd>


<dt>term</dt>
<dd>Character vector of term IDs annotated to corresponding genes.</dd>


<dt>min_genes</dt>
<dd>Minimum number of genes in gene sets.</dd>


<dt>max_genes</dt>
<dd>Maximum number of genes in gene sets.</dd>

</dl>

get_ontological_gene_sets: Create list of gene sets defined by ontological annotation

Description

Usage

Value

Arguments