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fisher exact using tidyr or dplyr approach

I have data dataframe with two groups, Tumor and Normal. for each site/row i want calculate fischer exact for using Methyl UnMethy between Tumor and Normal

I'm looking for how to transform data to calculate fisher exact for each site using dplyr approach.

methyl_dat <- data.frame(loci = c("site1", "site2", "site3", "site4"), 
           Methy.tumor = c(50, 5, 60, 12), 
           UnMethy.tumor = c(60, 0, 65, 5), 
           Methy.Normal = c(13, 5, 22, 3),
           UnMethy.Normal = c(86, 0, 35, 3) )

Here is Fischer exact strategy for site 1

              Normal
Tumor          Methyl  UnMethy
  Methy         50      13
  UnMethy       60      86
Solution

  • consider doing:

    apply(methyl_dat[-1], 1, \(x)fisher.test(matrix(x,2)), simplify = F)