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...art of the permutation test for a genome-wide association study). How can I run this process most efficiently? Is there any way to optimize R code? I have my data in a 2x2xN array (N ~ 5 K; eventually N will be ~ 500 K), and use apply inside the loop: > for (iter in 1:1000) { apply(data,3,fisherPval) } fisherPval <- function(x) { fisher.test(x)$p.value } Right now, it takes about 30 sec per iteration on an Intel Xeon 3.06GHz processor. Thanks in advance. -- Anna Pluzhnikov, PhD Section of Genetic Medicine Department of Medicine The University of Chicago --------------...