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    <h1>Filter GO/Reactome Gene Sets</h1>
    
    <div class="hidden name"><code>FilterGOTerms.Rd</code></div>
    </div>

    <div class="ref-description">
    <p>Subset gene sets based on GO/Reactome IDs.</p>
    </div>

    <div id="ref-usage">
    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">FilterGOTerms</span><span class="op">(</span></span>
<span>  term <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span>  spe <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"spe"</span><span class="op">)</span>,</span>
<span>  n.min <span class="op">=</span> <span class="fl">1</span>,</span>
<span>  n.max <span class="op">=</span> <span class="cn">Inf</span>,</span>
<span>  only.end.terms <span class="op">=</span> <span class="cn">F</span>,</span>
<span>  change.name <span class="op">=</span> <span class="cn">F</span>,</span>
<span>  parent <span class="op">=</span> <span class="cn">NULL</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="fu">FilterReactomeTerms</span><span class="op">(</span></span>
<span>  term <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span>  spe <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"spe"</span><span class="op">)</span>,</span>
<span>  n.min <span class="op">=</span> <span class="fl">1</span>,</span>
<span>  n.max <span class="op">=</span> <span class="cn">Inf</span>,</span>
<span>  only.end.terms <span class="op">=</span> <span class="cn">F</span>,</span>
<span>  change.name <span class="op">=</span> <span class="cn">F</span>,</span>
<span>  parent <span class="op">=</span> <span class="cn">NULL</span></span>
<span><span class="op">)</span></span></code></pre></div>
    </div>

    <div id="arguments">
    <h2>Arguments</h2>
    <dl><dt>term</dt>
<dd><p>GO/Reactome IDs, either as a character vector or matrix (with IDs in rownames). If NULL, the function will filter from the entire database.</p></dd>


<dt>spe</dt>
<dd><p>Species, either 'human' or 'mouse'. Default: getOption("spe").</p></dd>


<dt>n.min</dt>
<dd><p>Minimum number of genes in the gene set. Default: 1.</p></dd>


<dt>n.max</dt>
<dd><p>Maximum number of genes in the gene set. Default: Inf.</p></dd>


<dt>only.end.terms</dt>
<dd><p>Boolean indicating whether only return the end-level pathways or gene sets. Default: FALSE.</p></dd>


<dt>change.name</dt>
<dd><p>Boolean indicating whether to change the gene set names. Default: FALSE.</p></dd>


<dt>parent</dt>
<dd><p>ID or name of the parent (top-level) gene set in the GO/Reactome database. Default: NULL.</p></dd>

</dl></div>
    <div id="value">
    <h2>Value</h2>
    

<p>Returns a character vector or matrix, depending on the input.</p>
    </div>

    <div id="ref-examples">
    <h2>Examples</h2>
    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va">SeuratExtend</span><span class="op">)</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">options</a></span><span class="op">(</span>max.print <span class="op">=</span> <span class="fl">10</span>, spe <span class="op">=</span> <span class="st">"human"</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># Filter GO terms. For instance, select pathways under the category GO:0002376 (immune system process).</span></span>
<span><span class="va">terms</span> <span class="op">&lt;-</span> <span class="fu">FilterGOTerms</span><span class="op">(</span>parent <span class="op">=</span> <span class="st">"GO:0002376"</span><span class="op">)</span></span>
<span><span class="fu"><a href="RenameGO.html">RenameGO</a></span><span class="op">(</span><span class="va">terms</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># If you want to further restrict the number of genes in a pathway to be between 10 and 1000,</span></span>
<span><span class="co"># you can adjust the n.min and n.max parameters.</span></span>
<span><span class="va">terms2</span> <span class="op">&lt;-</span> <span class="fu">FilterGOTerms</span><span class="op">(</span>term <span class="op">=</span> <span class="va">terms</span>, n.min <span class="op">=</span> <span class="fl">10</span>, n.max <span class="op">=</span> <span class="fl">1000</span><span class="op">)</span></span>
<span><span class="fu"><a href="RenameGO.html">RenameGO</a></span><span class="op">(</span><span class="va">terms2</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># To only return the end-level pathways, set the only.end.terms parameter to TRUE.</span></span>
<span><span class="va">terms3</span> <span class="op">&lt;-</span> <span class="fu">FilterGOTerms</span><span class="op">(</span>term <span class="op">=</span> <span class="va">terms</span>, only.end.terms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
<span><span class="fu"><a href="RenameGO.html">RenameGO</a></span><span class="op">(</span><span class="va">terms3</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># Filter Reactome terms. For example, select pathways under the category R-HSA-168256 (Immune System).</span></span>
<span><span class="va">terms</span> <span class="op">&lt;-</span> <span class="fu">FilterReactomeTerms</span><span class="op">(</span>parent <span class="op">=</span> <span class="st">"R-HSA-168256"</span><span class="op">)</span></span>
<span><span class="fu"><a href="RenameGO.html">RenameReactome</a></span><span class="op">(</span><span class="va">terms</span><span class="op">)</span></span></code></pre></div>
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