Body: <p>I have been dealing with this problem for the past 48 hrs. I do not know what is it, which prevents the function from assessing the parameters it gets passed.</p>
  <pre class="lang-r prettyprint-override"><code>params &lt;- GSEAGOHyperGParams(name = &quot;My Custom GSEA based annot Params&quot;,
                                geneSetCollection = new_df,
                                geneIds = new_df$GOIds,
                                universeGeneIds = gene_universe,
                                ontology = &quot;BP&quot;,
                                pvalueCutoff = 0.05,
                                conditional = FALSE,
                                testDirection = &quot;over&quot;,
                                organism = &quot;human&quot;)
  Error in (function (classes, fdef, mtable)  : 
    unable to find an inherited method for function ‘geneIdType’ for signature ‘&quot;character&quot;’ 
  </code></pre>
  <p>In an example below (edited), you could see that it is character, but either way if I change it do integer, it does not work. Maybe character vector ?</p>
  <pre class="lang-r prettyprint-override"><code>&gt; str(new_df)
  'data.frame':   68 obs. of  4 variables:
   $ GOIds   : chr  &quot;GO:0001725&quot; &quot;GO:0001725&quot; &quot;GO:0003779&quot; &quot;GO:0005515&quot; ...
   $ evi1    : chr  &quot;IBA&quot; &quot;IDA&quot; &quot;IEA&quot; &quot;IPI&quot; ...
   $ genes1  : chr  &quot;23002&quot; &quot;23002&quot; &quot;23002&quot; &quot;23002&quot; ...
   $ ontology: chr  &quot;CC&quot; &quot;CC&quot; &quot;MF&quot; &quot;MF&quot; ...
  </code></pre>
  <p>Same goes, when I try to cast it into an integer type by using <code>as.integer()</code>.
  Any suggestions for this function from an R package <code>clusterProfiler</code>?
  I believe this is from this package, but there could be one or two other packages, where this function maybe present.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-03-28T17:58:01.963Z
Comments.Text: What does `ensembl_gene_ids` have to do with your function call?
Comments.UserDisplayName: Ram RS
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-03-28T20:07:01.773Z
Comments.Text: Hi! What package are you using in R? Thanks
Comments.UserDisplayName: Sarah
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-03-28T23:01:19.030Z
Comments.Text: Edited the query and answered to both ! Thanks !
Comments.UserDisplayName: aleksk31
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-03-29T12:16:47.517Z
Comments.Text: According to the documentation, geneSetCollection should be a GeneSetCollection Object : https://www.rdocumentation.org/packages/Category/versions/2.38.0/topics/GSEAGOHyperGParams
Comments.UserDisplayName: Basti
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-03-30T04:37:58.823Z
Comments.Text: Okay, thank you every1. With a duplicate answer from Stack Overflow, I was able to succeed a bit only to stumble upon a different issue, for some reason the function `OverMF <- hyperGTest(params2). Error in getUniverseHelper(probes, datPkg, entrezIds) : 
    After filtering, there are no valid IDs that can be used as the Gene universe.
    Check input values to confirm they are the same type as the central ID used by your annotation package.
    For chip packages, this will still mean the central GENE identifier used by the package (NOT the probe IDs).`
Comments.UserDisplayName: aleksk31
Tags: <r><kegg><gene-ontology><go>
Title: Gene set enrichment ontology analysis issue
ThreadText: # Gene set enrichment ontology analysis issue
  
  (Asked by: username_0 on 2024-03-28)
  
  I have been dealing with this problem for the past 48 hrs. I do not know what is it, which prevents the function from assessing the parameters it gets passed.
  
  ```r
  params <- GSEAGOHyperGParams(name = "My Custom GSEA based annot Params",
                                geneSetCollection = new_df,
                                geneIds = new_df$GOIds,
                                universeGeneIds = gene_universe,
                                ontology = "BP",
                                pvalueCutoff = 0.05,
                                conditional = FALSE,
                                testDirection = "over",
                                organism = "human")
  Error in (function (classes, fdef, mtable)  : 
    unable to find an inherited method for function ‘geneIdType’ for signature ‘"character"’ 
  
  ```
  
  In an example below (edited), you could see that it is character, but either way if I change it do integer, it does not work. Maybe character vector ?
  
  ```r
  > str(new_df)
  'data.frame':   68 obs. of  4 variables:
   $ GOIds   : chr  "GO:0001725" "GO:0001725" "GO:0003779" "GO:0005515" ...
   $ evi1    : chr  "IBA" "IDA" "IEA" "IPI" ...
   $ genes1  : chr  "23002" "23002" "23002" "23002" ...
   $ ontology: chr  "CC" "CC" "MF" "MF" ...
  
  ```
  
  Same goes, when I try to cast it into an integer type by using `as.integer()`.
  Any suggestions for this function from an R package `clusterProfiler`?
  I believe this is from this package, but there could be one or two other packages, where this function maybe present.
  
  **Tags:** r, kegg, gene-ontology, go
  
  > **Comments:**
  > **username_1**: What does `ensembl_gene_ids` have to do with your function call?  
  > **username_2**: Hi! What package are you using in R? Thanks  
  > **username_0**: Edited the query and answered to both ! Thanks !  
  > **username_3**: According to the documentation, geneSetCollection should be a GeneSetCollection Object : https://www.rdocumentation.org/packages/Category/versions/2.38.0/topics/GSEAGOHyperGParams  
  > **username_0**: Okay, thank you every1. With a duplicate answer from Stack Overflow, I was able to succeed a bit only to stumble upon a different issue, for some reason the function `OverMF <- hyperGTest(params2). Error in getUniverseHelper(probes, datPkg, entrezIds) :    After filtering, there are no valid IDs that can be used as the Gene universe.   Check input values to confirm they are the same type as the central ID used by your annotation package.   For chip packages, this will still mean the central GENE identifier used by the package (NOT the probe IDs).`  
  
  ---
  
  ## 0 answers
  
  