Hi Anna, I am not really answering your question, but, here goes my (unsolicited) suggestion. Some time back I did some simulations to see how the HWE tests performed. In particular I compared the exact test and the chi squared test. Look at the attached figure Rplots.ps. I saw that for null simulations with 40 individuals, the HWE chi squared test was reasonably close to the (expected) uniform distribution. However this was obtained using the function HWE.chisq(X, simulate.p.value=F), the default seemed to have some issues. Hence my suggestion would be, if you feel comfortable, to replace the exact test with a chi sq test, at least at the screening level. Once you identify a set of SNPs with "small" p-values, you could follow them up with the exact test.
-- Ritwik Sinha Graduate Student Epidemiology and Biostatistics Case Western Reserve University http://darwin.cwru.edu/~rsinha <http://darwin.cwru.edu/%7Ersinha>
Rplots.ps
Description: PostScript document
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