wtest: an R Package for Testing Main and Interaction Effect in Genotype Data with Binary Traits
Rui Sun, Billy Chang, Benny Chung-Ying Zee, Maggie Haitian Wang
TL;DR
wtest is an R package designed for efficient and accurate testing of main and interaction effects of SNPs in genome-wide data, facilitating genetic association studies with a user-friendly interface.
Contribution
It introduces a scalable, fast, and accurate implementation of the W-test for genetic effect analysis, including diagnostic tools and flexible testing options.
Findings
Provides fast p-value estimation for SNP effects
Enables interaction effect testing in genome-wide data
Offers diagnostic checks for distribution assumptions
Abstract
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
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Taxonomy
TopicsGenetic Associations and Epidemiology · Genetic Mapping and Diversity in Plants and Animals · Genetics and Plant Breeding