Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-04-26T20:49:29.370Z
Answers.LastActivityDate: 2018-04-26T20:49:29.370Z
Answers.UserDisplayName: Devon Ryan
Body: <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>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-04-26T19:28:55.447Z
Comments.Text: That's funny, I asked the same question today on bioconductor [support](https://support.bioconductor.org/p/108311/) about the `level` argument. I can tell you what `ont` stands for, though. It is the sub-ontology, MF = molecular function, BP = biological process, and CC = cellular component. Read more about it at the [GO consortium](http://www.geneontology.org/page/ontology-documentation).
Comments.UserDisplayName: benn
Tags: <rna-seq><groupgo><clusterprofiler>
Title: groupGO parameters explanation (ont and level)
ThreadText: # groupGO parameters explanation (ont and level)
  
  (Asked by: username_0 on 2018-04-26)
  
  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`...
  
  **Tags:** rna-seq, groupgo, clusterprofiler
  
  > **Comments:**
  > **username_1**: That's funny, I asked the same question today on bioconductor [support](https://support.bioconductor.org/p/108311/) about the `level` argument. I can tell you what `ont` stands for, though. It is the sub-ontology, MF = molecular function, BP = biological process, and CC = cellular component. Read more about it at the [GO consortium](http://www.geneontology.org/page/ontology-documentation).  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2018-04-26. Score: 1 | Accepted answer
  
  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](http://geneontology.org/page/ontology-structure#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](https://www.biostars.org/p/237816/) 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).
  
  
  ---
  
  