I am interested in using using variant proportions as input to perform Gene Set Enrichment Analysis (GSEA). Is anyone aware of a Bioconductor package in R or any other tool that can help me do GSEA analysis using variant proportions data as input rather than the typical RNA seq expression data. I have two different phenotype groups which I want to compare and I can have the proportion data transformed if needed. I also intend to combine these results with RNA seq expression data results.
Doing some research, I have come across many papers using p values but I am mainly interested in using variant data input.
Any help would be greatly appreciated. Thanks,