text: user2005: I need to use groupGO in clusterProfiler to find functional profile of a list of genes, and I am having trouble finding out what some parameters of the function mean and which I should select for my specific case.
  The function is defined as:
  groupGO(gene, OrgDb, keyType = "ENTREZID", ont = "CC", level = 2,
    readable = FALSE)
  
  I have mouse genes dataset. What I should select for ont and level parameters? What does ont types: MF, BP, CC mean? What is level? Where I could find this info? It is definitely not in the vignette...
  
  user77: As mentioned in the comments MF is molecular function, BP is biological process and CC is cellular compartment. These are the 3 domains of the ontologies. The level refers to the level in the ontology graph. In the example in that link, pigmentation would be level 1, pigmentation during development level 2, regulation of pigmentation during development is level 3 and so on. You can find more discussion of this in this post on biostars from a year ago.
  Regarding the exact settings you should use, I don't personally find CC to be an informative domain. The first couple levels are typically too generic to be useful and they'll include too many genes anyway for you to likely pick up any changes. I'd start around level 3 and see how things go (in other programs you would get all of the levels and domains at once).
  
original_text: 2005: <p>I need to use <code>groupGO</code> in <code>clusterProfiler</code> to find functional profile of a list of genes, and I am having trouble finding out what some parameters of the function mean and which I should select for my specific case.</p>
  
  <p>The function is defined as:</p>
  
  <pre><code>groupGO(gene, OrgDb, keyType = "ENTREZID", ont = "CC", level = 2,
    readable = FALSE)
  </code></pre>
  
  <p>I have mouse genes dataset. What I should select for <code>ont</code> and <code>level</code> parameters? What does <code>ont</code> types: <code>MF</code>, <code>BP</code>, <code>CC</code> mean? What is <code>level</code>? Where I could find this info? It is definitely not in the <code>vignette</code>...</p>
   77: <p>As mentioned in the comments <code>MF</code> is <code>molecular function</code>, <code>BP</code> is <code>biological process</code> and <code>CC</code> is <code>cellular compartment</code>. These are the 3 domains of the ontologies. The <code>level</code> refers to the level in the <a href="http://geneontology.org/page/ontology-structure#graph" rel="nofollow noreferrer">ontology graph</a>. In the example in that link, <code>pigmentation</code> would be level 1, <code>pigmentation during development</code> level 2, <code>regulation of pigmentation during development</code> is level 3 and so on. You can find more discussion of this in <a href="https://www.biostars.org/p/237816/" rel="nofollow noreferrer">this post</a> on biostars from a year ago.</p>
  
  <p>Regarding the exact settings you should use, I don't personally find <code>CC</code> to be an informative domain. The first couple levels are typically too generic to be useful and they'll include too many genes anyway for you to likely pick up any changes. I'd start around level 3 and see how things go (in other programs you would get all of the levels and domains at once).</p>
  