wtest: an R Package for Testing Main and Interaction Effect in Genotype Data with Binary Traits

This R package evaluates main and pair-wise interaction effect of single nucleotide polymorphisms (SNPs) via the W-test, scalable to whole genome-wide data sets. The package provides fast and accurate p-value estimation of genetic markers, as well as diagnostic checking on the probability distributions. It allows flexible stage-wise or exhaustive association testing in a user-friendly interface. Availability: The package is available in CRAN, or from website: http://www2.ccrb.cuhk.edu.hk/wtest Background Single nucleotide polymorphism (SNPs) association testing is an important step for selecting potential drug target and understanding gene function in disease etiology. Current methods mainly incorporate classical probability distributions or permutation tests to calculate p-values. However, tests based on theoretical probability distributions might have affected power in the challenging genetic environment of sparse data and complicated genetic architectures; on the other hand, tests