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Question: How to select a specific onthology after runing enrichGO for all 3 onthology
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gravatar for MAP
4 months ago by
MAP0
MAP0 wrote:

Hi all,

I have run a GO enrichment analysis using enrichGO() for all 3 onthologies at once:

analysis <- enrichGO(gene = names_down_uniprot, OrgDb = "org.Mm.eg.db",
   keyType = "UNIPROT", ont = "ALL", pvalueCutoff = 0.05,
   pAdjustMethod = "fdr", universe = background_uniprot, qvalueCutoff = 0.25,
   minGSSize = 10, maxGSSize = 500, readable = FALSE, pool = FALSE)

The result looks good and as expected.

Do anyone now how to subset this results for a specific onthology? My idea is to represent graphically (using  barplot, cnetplot, etc) only one of of them (in particular BP).

Thanks in advance,

Miguel

 

ADD COMMENTlink modified 4 months ago • written 4 months ago by MAP0

I don't think clusterProfiler has that functionality. Why not just run the `enrichGO` for each ontology category?

ADD REPLYlink written 4 months ago by emilliman40

Thanks for your reply emilliman4.

I am actually doing what you suggested, but the option I was looking for could simplify a lot my workflow.

It would be great if they can include this option in future updates. 

ADD REPLYlink modified 3 months ago • written 3 months ago by MAP0
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