How to select a specific onthology after runing enrichGO for all 3 onthology

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MAP ▴ 10

@map-16849

Last seen 6.3 years ago

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

enrichGO clusterprofiler • 2.2k views

ADD COMMENT • link 6.4 years ago MAP ▴ 10

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

ADD REPLY • link 6.3 years ago emilliman4 • 0

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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 REPLY • link 6.3 years ago MAP ▴ 10

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