Hi,

My query is regarding permutation test and reshuffling of genotype/phenotype
data
I have been using the haplo.stats package of R. for haplotype analysis and I
would like to perform an analysis which I'm requesting your advice.
I have a data set of individuals genotyped for 12 SNP and a dichotomous
phenotype.
At first, I have tested each of those SNP independently in order to bypass
multiple testing issues and
I have found that 5 out of those 12 SNP had a p value <0.05.
The analysis that I would like to run is a permutation simulation (lets say
10,000 times) that will estimate the probability to receive
significant results by chance for 5 SNP or more.
I'm aware that permutation test are available in R however, I could not find
the way of writing the right algorithm
that will count at each run only the cases by which at least 5 SNP (out of
12) were significant.
Any assistance on that matter will be most appreciated.

Many thanks,

Jonathan

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