Fisher's Exact Test for Competitive Gene-set Enrichment
Code
Function to generate FET p-values and other simple statistics
Fisher_Enrichment_13.R- Function to empirically estimate FDR q-value (random generation of experimental gene-set)
enr.df <- f.Enr_Fisher ( GS.ls = , # list, slot names = gene-set IDs, slot content = gene IDs GS_names.chv = , # character array, values = gene-set IDs, names = gene-set full names exp.genes = , # character array, values = experimental gene IDs uni.genes = # character array, values = all the genes in the platform ) enr.df$FDR <- f.Fisher_FDR ( GS.ls = , # as above exp.genes = , # as above uni.genes = , # as above pval_obs.nv = enr.df$pvalue, iter.n = , # numeric value (default 2000) )