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Skat sequence kernel

Sequence Kernel Association Test (SKAT) The Sequence Kernel Association Test (SKAT) is a variance-component test for genetic association analysis. SKAT evaluates the distribution of genetic effects of a group of variants on continuous or dichotomous traits. SKAT detects variants with both positive and negative effects. You can install the SKAT R-package on MS Windows, UNIX/Linux, and Mac OSX. If you don’t know how to install an R-package, please see here. SKAT-O: To run SKAT-O, please set method=”optimal.adj” in the SKAT function, which provides a better type I error control in tail areas then method=”optimal” Combined effect of common and rare variants: SKAT is a regression method to test for association between genetic variants (common and rare) in a region.

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SKAT is a SNP-set (e.g., a gene or a region) level test for association between a set of rare (or common) variants and dichotomous or quantitative phenotypes. For rare variant analysis from sequencing association studies, GMMAT performs the variant Set Mixed Model Association Tests (SMMAT), including the burden test, the sequence kernel association test (SKAT), SKAT-O and an efficient hybrid test of the burden test and SKAT, based on user-defined variant sets.

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(2011). Rare-variant association testing for sequencing data with the sequence kernel association test. American Journal of Human Genetics 89:82-93.. proposed the sequence kernel association test (SKAT), which builds upon the kernel ma-chine regression framework, to test rare variants associations.

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22 Jun 2018 Abstract The sequence kernel association test (SKAT) is widely used to test for associations between a phenotype and a set of genetic variants Kernel properties. Hilbert spaces. Convex cone, distances, norms · Regularization and features. Shotgun approach · Hash kernels. Application - spam filtering.

References: 2016-07-07 · The sequence kernel association test (SKAT) is probably the most popular statistical test used in rare-variant association studies. Its null distribution involves unknown parameters that need to be estimated. 2015-09-30 · SKAT: SNP-Set (Sequence) Kernel Association Test.
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Description. Test for association between a set of SNPS/genes and continuous or dichotomous phenotypes Rare variants test: Variance component test. Sequence Kernel Association Test ( SKAT).

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For rare variant analysis from sequencing association studies, GMMAT performs the variant Set Mixed Model Association Tests (SMMAT), including the burden test, the sequence kernel association test (SKAT), SKAT-O and an efficient hybrid test of the burden test and SKAT, based on user-defined variant sets.

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