Wondering if I could use gseGO output from R and transfer it to use in enrichment map?

[muyusitu]

Hello,

I have been working on R generating my GSEA output by using the gseGO function from the clusterprofiler R package. However, I had a lot of issues trying to modify or set my data to be plotted on enrichment map by using the emcommand from the RCy3 package. I was wondering if you could provide insight into what I can do to visualize my GSEA data to the enrichment map?

[risserlin]

I have never used clusterprofiler gseGO function. What is the format of the file that you are trying to convert to a enrichmentmap generic format? Does clusterprofiler give you access to the geneset definition file?

[muyusitu]

Well gseGo outputs GSEA data so I have been able to get my data to map from R to enrichment map but for some reason, it won't accept my NES values and it gets reverted to a 1 for all rows.

I don't think it gives me access to a geneset definition file. Basically, I give the function, what ontology I am looking for, number of permutations, min and max of Gene Set Size, cutoffs, and organism I am working with.