Clusterprofiler object 'GO2ONT' not found
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Entering edit mode
8 weeks ago

Seems like the new update (3.18.1) of Clusterprofiler no longer automatically matches GO IDs to ontologies

enrichGO(gene=my_gene_ids, keyType = "FLYBASE", OrgDb = org.Dm.eg.db, ont="ALL", pAdjustMethod = "BH", qvalueCutoff = 0.05, readable = TRUE)
Error in get("GO2ONT", envir = GO_DATA) : object 'GO2ONT' not found

I tried to create an object for GO2ONT, but in order to retrieve GO IDs for this object, I need to use the get_GO_data function. Looks like this function is no longer found in the Clusterprofiler package.

GO_DATA <- get_GO_data("org.Dm.eg.db", "ALL", "SYMBOL") 
Error in get_GO_data("org.Dm.eg.db", "ALL", "SYMBOL") : 
  could not find function "get_GO_data"
get_GO_data go2ont enrichgo clusterprofiler GO • 183 views
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Entering edit mode
7 weeks ago

A week later, the enrichGO function is now working as intended. I guess that resolves the issue, though not very satisfactorily. I'll leave this post up in case someone else runs into the same error.

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