I'm new to these forums, but hoping you can help me with a question.
I am using phyper in R to compute p values that assess the significance of overlapping gene sets, though from whole exome sequencing results, not gene expression data.
1-phyper((#overlaps-1), disease list size, (total # genes-disease list size), PPI list size) example: 1-phyper((9-1), 353, 20000-353, 182)
where my PPI list size is the # of genes in my own dataset and disease list size is the number of genes in the gene set of interest.
I have performed a Bonferroni Correction to correct for multiple comparisons/tests, but feel like the proper way to assess significance is using a permutation test. I am wondering whether folks have good recommendations of R packages or scripts that will perform this kind of test WITHOUT gene expression data, and in general feedback about how to perform the permutation test. I have little statistical knowledge and little experience using R.
Thanks for any help you can give me!