Hello

In this paper

https://www.biorxiv.org/content/10.1101/082552v1.full

They are saying

For any pair of pathways, we used the one-sided Fisher’s exact test to determine the significance of their co-mutation.

If we have a matrix of pathways in rows and samples in columns and we have how many genes specific to each pathway have been mutated in each samples like below

How Fisher's exact test can say if any given pairs of pathways are co-mutated?

Can somebody pease solve this in my mind

In my understanding

> fisher.test(x = matrix(
  c(
    Total number of genes related to pathway A,
    pathwayA_mutated_samples,
   Total number of genes related to pathway B,
    pathwayB_mutated_samples
  ),
  nrow = 2
))

Would say if pathways A and B are differently disturbed

But I can not understand how I can say they are co -mutated