A novel power-based approach to Gaussian kernel selection in the kernel-based association test

Abstract

Kernel-based association test (KAT) is a widely used tool in genetics association analysis. The performance of such a test depends on the choice of kernel. In this paper, we study the statistical power of a KAT using a Gaussian kernel. We explicitly develop a notion of analytical power function in this family of tests. We propose a novel approach to select the kernel so as to maximize the analytical power function of the test at a given test level (an upper bound on the probability of making a type I error). We assess some theoretical properties of our optimal estimator, and compare its performance with some similar existing alternatives using simulation studies. Neuroimaging data from an Alzheimer’s disease study is also used to illustrate the proposed kernel selection methodology.