SPS: A Simulation Tool for Calculating Power of Set‐Based Genetic Association Tests |
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| Authors: | Jiang Li Pak Chung Sham Youqiang Song Miaoxin Li |
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| Affiliation: | 1. Department of Biochemistry, the University of Hong Kong, Pokfulam, Hong Kong;2. Department of Psychiatry, the University of Hong Kong, Pokfulam, Hong Kong;3. The Centre for Genomic Sciences, the University of Hong Kong, Pokfulam, Hong Kong;4. State Key Laboratory for Cognitive and Brain Sciences, the University of Hong Kong, Pokfulam, Hong Kong;5. The Centre for Reproduction, Development and Growth, the University of Hong Kong, Pokfulam, Hong Kong |
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| 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/ . |
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| Keywords: | set‐based association test power complex disease simulation meta‐analysis |
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