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)

  Fisher_Enrichment_FDR_13_1.R

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)
                )