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....@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 > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
