Displaying 1 result from an estimated 1 matches for "fisherpval".
2005 Nov 18
2
(no subject)
...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
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