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MCPerm: Monte Carlo SNP permutation
Monte Carlo permutation method for SNP multiple test correlation
...However, it relies on the original single nucleotide polymorphism (SNP) genotypes and phenotypes data to perform a large number of random shuffles, and thus it is computationally intensive, especially for genome-wide association study (GWAS). To improve the calculation speed without changing the size of the TradPerm p-value, we developed a Monte Carlo permutation (MCPerm) method as an efficient alternative to TradPerm. Methods: MCPerm does not need to shuffle the original genotypes and phenotypes data. It uses Monte Carlo method, employs two-step hypergeometric distribution to generate the random number of genotypes (AA, Aa and aa) in cases and controls.
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