How can I peform fisher-exact test for mutation co-occurance in large datasets?

Question

[joetaylor268]

I am new to R and am having some trouble in performing Fisher exact test for mutation co-occurrences in large datasets.

My matrix consists of 278 samples with mutation data for 150 genes (278x150) (cell values of 1 for mutant, 0 for normal). I am trying to find an appropriate way of generating p-values for pairwise mutation overlaps. Because of this sequential analysis it would also be important to perform multiple-correction testing (FDR)? I am aware that phyper (hypergeometric test) is essentially a one-tailed fisher test - so that may be a possible route?

Is there an easy way of doing this rather than manually generating 2x2 contingency tables for each pairwise mutation combination?