Cluster profiler GSEA data frame to gseaResult and interpretation of results

Question

[Pahi]

Hi!

I started to work with RNA-seq and I would like to make a GSEA analysis.

I use the Cluster profiler package to do the GSEA analysis, with the gseGO. I get my results and everything works fine, but I have some questions in my head.

1. gseGO requires ordered gene list as an input. But is the result of the gseGO is ordered? As I see if I convert the result to data frame that there is no pattern in the order of GSEA results. How should I handle the result? If I plot the first 5 ID from the result, are they the most enriched genes of the analysis? What parameter show that these are the most enriched ones, or the ones worth my attention?

1. I started to play with the data I got from the gseGO. I converted it to a df and started to order the values (ES, pvalue, rank). Now I have a few df, but I would like to convert it back to gseaResult, otherwise the gseaplot2 (from enrichplot package) won't work. Any idea to this? Or is there a package to handle my problem?

Sorry for the long post and questions! Thank you for your help and time in advance!