[R] permutation test - query

[Juliet Hannah]

You may find the multtest package helpful. It implements methods from
Westfall and Young (Resampling based multiple testing).



On Mon, Aug 31, 2009 at 5:37 AM, Yonatan
Nissenbaum<yoni.nis at mail.huji.ac.il> wrote:
> 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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>
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