GMMAT

swMATH45216CRANGMMATMaRDI QIDQ1333108FDOQ1333108

Generalized Linear Mixed Model Association Tests

Matthew Conomos, Han Chen, Duy Pham

Last update: 17 November 2023

Copyright license: GNU General Public License

Software version identifier: 1.4.0, 1.4.1, 1.4.2

Source code repository: https://github.com/cran/GMMAT

Description

Perform association tests using generalized linear mixed models (GLMMs) in genome-wide association studies (GWAS) and sequencing association studies. First, GMMAT fits a GLMM with covariate adjustment and random effects to account for population structure and familial or cryptic relatedness. For GWAS, GMMAT performs score tests for each genetic variant as proposed in Chen et al. (2016) <doi:10.1016/j.ajhg.2016.02.012>. For candidate gene studies, GMMAT can also perform Wald tests to get the effect size estimate for each genetic variant. For rare variant analysis from sequencing association studies, GMMAT performs the variant Set Mixed Model Association Tests (SMMAT) as proposed in Chen et al. (2019) <doi:10.1016/j.ajhg.2018.12.012>, 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.

Cites work

• Control for Population Structure and Relatedness for Binary Traits in Genetic Association Studies via Logistic Mixed Models
• Efficient Variant Set Mixed Model Association Tests for Continuous and Binary Traits in Large-Scale Whole-Genome Sequencing Studies

Cited In (2)

• RsqMed
• MAGEE

This page was built for software: GMMAT