search

YuLab-SMU / clusterProfiler

:bar_chart: A universal enrichment tool for interpreting omics data
https://yulab-smu.top/biomedical-knowledge-mining-book/
1.02k stars 256 forks source link

How to select a specific onthology after runing enrichGO for all 3 onthology #158

Open Mndin opened 6 years ago

Mndin commented 6 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).

If this option doesn't exist, I think it could be nice if it is included in future updates.

Thanks in advance and congratulations for creating this incredible package,

Mndin

xz289 commented 5 years ago

I got similar questions to ask, which I had ran the enrichGO for BP only and get lots of pathways, but i am only interested in some of them and want to creat cnetplot/emaplot/upsetplot... The difficulty is how to get the sub object of the enrichGO result. So far I can only have the subset of the data frame but not the enrich object and can not produce the above plot. Do you have any suggestions or already have an idea for this problem? Regards Hui