Education / Mathematics

MCPerm: Monte Carlo SNP permutation - 1.1.2

MCPerm: A Monte Carlo permutation method for multiple test correlation in case-control association studyTraditional permutation (TradPerm) test is an important non-parametric analysis method which can be treated as the gold standard for multiple test





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Current Version: 1.1.2
License: Freeware
Downloads: 8


Software Description:
MCPerm: A Monte Carlo permutation method for multiple test correlation in case-control association studyTraditional permutation (TradPerm) test is an important non-parametric analysis method which can be treated as the gold standard for multiple testing corrections in case-control association study. 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.

Lucent Public License Version 1.02
Software Requirements:
No specific requirements

This software is designed to run on the following operating systems:

Download Link of MCPerm: Monte Carlo SNP permutation 1.1.2:

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