Is there any way to reduce the redundancy of a set of GO terms when working with a non-reference organism? I mean something similar to REVIGO. The problem with the last is that has a limit in the number of GO terms that can be submitted.
I have read the documentation of GoSemSim and it seems that can work only with supported organisms (though I expected that maybe it would have a function like buildGOmap from clusterProfiler). I have tried to work with goProfiles too, but there is no way to make it work without a orgPackage option (though in the examples from the vignettes it is not used nor mentioned).
edit: I finally was able to make goProfiles work with the basicProfile() parameter idType = "GOTermsFrame". This way, it ignores the orgPackage and anotPackage parameters since you provide the GeneID <--> GOID mappings goProfiles needs.
Thank you in advance
ps.: I have already done enrichment analysis (with topGO) and it is not what I mean in this post.