Hello friends, I downloaded gistic 2.0 file from TCGA biolink, and I want to do copy number variation analysis for two groups. My file has about 20000 rows (first row is gene IDs), and about 600 columns that are patient names (two groups : 360 vs 240). I am trying to do this with Fisher's exact test in R. I did not find any other method to do in R. for fisher's exact test, I need to have contingency table. I don't have any idea how to make contingency table for a large file. Is my method correct at all? Anyone can help me with making table and doing this test please?

Thanks