SPS: A Simulation Tool for Calculating Power of Set-Based Genetic Association Tests

ABSTRACT Set‐based association tests, combining a set of single‐nucleotide polymorphisms into a unified test, have become important approaches to identify weak‐effect or low‐frequency risk loci of complex diseases. However, there is no comprehensive and user‐friendly tool to estimate power of set‐based tests for study design. We developed a simulation tool to estimate statistical power of multiple representative set‐based tests (SPS). SPS has a graphic interface to facilitate parameter settings and result visualization. Advanced functions include loading real genotypes to define genetic architecture, set‐based meta‐analysis for risk loci with or without heterogeneity, and parallel simulations. In proof‐of‐principle examples, SPS took no more than 3 sec on average to estimate the power in a conventional setting. The SPS has been integrated into a user‐friendly software tool (KGG) as an independent functional module and it is freely available at http://statgenpro.psychiatry.hku.hk/limx/kgg/.