How to perform enrichment (overrepresentation) using custom path sets in R
Hi,
I am trying to do enrichment analysis (specifically using ORA) for metabolites with own path sets. For example, I have compounds expression data with compound names/HMBI/KeggID, and I have a custom compound set, which have 200+pathways with corresponding compounds. I would like to do ORA enrichment on the compound expression data using my own custom compound set.
I know clusterprofiler has enricher function andI tried it, but it seemed only work for genes. Is there any other packages or function I can do enrichment using own pathways set? My goal is to see what pathways I can map using ORA.
Thank you in advance.
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Can you include an example of you metabolite values and your path sets? Also, what problem did you have with clusterProfiler?
I think MSEA is working. I will delete this post