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taniawyss committed Mar 11, 2024
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Expand Up @@ -693,7 +693,7 @@ <h2 id="exercise-2-gene-set-enrichment-analysis-gsea">Exercise 2 - Gene set enri
<span class="c1"># How to obtain the list of all genes included in a GO term:</span>
<span class="n">GO_NK_Th</span><span class="o">@</span><span class="n">geneSets</span><span class="o">$</span><span class="n">`GO:0002250`</span>
</code></pre></div>
<p>As you will see later in the course, objects of type enrichResult or gseaResult generated by clusterProfiler functions can be used directly in some visualization functions. Therefore, you could save your full output object also to allow for easy visualization.</p>
<p>As you will see later in the course, objects of type <code>enrichResult</code> or <code>gseaResult</code> generated by <code>clusterProfiler</code> functions can be used directly in some visualization functions. Therefore, you could save your full output object also to allow for easy visualization later.</p>
<div class="highlight"><pre><span></span><code><span class="c1"># export full object</span>
<span class="nf">saveRDS</span><span class="p">(</span><span class="n">GO_NK_Th</span><span class="p">,</span> <span class="s">&quot;GO_NK_Th.rds&quot;</span><span class="p">)</span>

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