GSEA Result Visualization in R

Question

[Cortney]

Hello, I have performed GSEA analysis using the Broad's GSEA software. I now want to create a running enrichment score figure that includes my top 4 gene sets using the 'enrichplot' package in R. (example picture below)

However, I cannot figure out how to format the data received from the Broad's GSEA software in a way that it is successfully called by the gseaplot2 function. I keep receiving this error:

Error in FUN(X[[i]], ...) : 
  trying to get slot "geneList" from an object (class "data.frame") that is not an S4 object

How do I format my GSEA results to include the ranked gene list and gene sets for this visualization?

Answer 1

[jared.andrews07]

That functions expects the output from the gseDO function from DOSE.

[Cortney]

Yes, but I am trying to use my results from the Broad's software for consistency. I am also using a custom gene set annotation list. Do you know how I can format my ranked gene list and custom gene sets? I cannot figure out how to get the gene names from my list to map to the entrez gene id while also keeping my gene sets.