1 f.Fisher_FDR <- function (exp.genes, uni.genes, GS.ls, pval_obs.nv, iter.n = 2000)
   2     {
   3 
   4     cat ("\n")
   5 
   6     # 1) PRE-PROCESSING
   7 
   8     # Reduce everything to the universe
   9 
  10     f.int_uni <- function (input.genes)
  11         {return (intersect (input.genes, uni.genes))}
  12 
  13     GS.ls <- lapply (GS.ls, f.int_uni)
  14 
  15     exp.genes <- intersect (exp.genes, uni.genes)
  16 
  17     # 2) COMPUTING
  18     
  19     exp.n <- length (exp.genes)
  20     uni.n <- length (uni.genes)
  21 
  22     dummy.ls <- as.list (rep (exp.n, iter.n))
  23     
  24     f.sample_Unit <- function (l.n)
  25         {return (sample (uni.genes, l.n))}
  26     
  27     exp_r.ls <- lapply (dummy.ls, f.sample_Unit)
  28 
  29     output.nv <- numeric (3)
  30 
  31     f.Fisher_PvalR_Unit <- function (exp.genes)
  32         {
  33             
  34         f.Enr_Fisher_Unit <- function (GS.genes)
  35             {
  36             enr.n    <- length (intersect (exp.genes, GS.genes))
  37             GS.n     <- length (GS.genes)
  38 
  39             table.mx <- matrix (
  40                     ncol = 2, 
  41                     nrow = 2, 
  42                     data = c (
  43                         enr.n, 
  44                         GS.n  - enr.n, 
  45                         exp.n - enr.n, 
  46                         uni.n - (GS.n + exp.n - enr.n)
  47                         ), 
  48                     byrow = T
  49                     )
  50 
  51             pvalue.n <- fisher.test (table.mx, alternative = "greater")$p.value
  52             return (pvalue.n)
  53             }
  54 
  55         cat ("r")
  56             
  57         pvalues.nv <- sapply (GS.ls, f.Enr_Fisher_Unit)
  58         return (pvalues.nv)
  59         }
  60     
  61     pval_r.mx <- sapply (exp_r.ls, f.Fisher_PvalR_Unit)
  62     
  63     pval_obs.ls <- as.list (pval_obs.nv)
  64     
  65     f.count_Unit <- function (thr.n)
  66         {
  67         rand.n <- sum (pval_r.mx <= thr.n) / iter.n
  68         obs.n  <- sum (pval_obs.nv <= thr.n)
  69         return (rand.n / obs.n)
  70         }
  71     
  72     fdr.nv <- sapply (pval_obs.ls, f.count_Unit)
  73     
  74     return (fdr.nv)
  75         
  76     }