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.