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affs
2006 Jun 05
3
Fastest way to do HWE.exact test on 100K SNP data?
...to repeat this procedure multiple times (~1000) permuting the cases and
controls (affection status). It seems straightforward to implement it like this:
#############################################
for (iter in 1:1000) {
set.seed(iter)
# get the permuted affection status
permut <- sample(affSt)
for (j in 1:nSNPs) {
test <- tapply(all.geno[[j]], permut, HWE.exact)
pvalControls[j] <- test$"1"$p.value
pvalCases[j] <- test$"2"$p.value
}
}
##############################################
The problem is that it takes ~1 min/iteration (on AMD Opteron...