example

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.

Han Chen

GMMAT

Generalized Linear Mixed Model Association Tests

Matthew Conomos

Duy Pham

Arthor Gilly

Robert Gentleman

Ross Ihaka

The R Core Team 

The R Foundation 

Eric Biggers

Tino Reichardt

Meta Platforms, Inc. and affiliates 

example function

Contains the following objects:<dl>
 <dt>pheno</dt>
<dd>a data frame of 400 observations from a cross-sectional study with 5 variables: id, disease, trait, age and sex.</dd> <dt>pheno2</dt>
<dd>a data frame of 2,000 observations from a longitudinal study with 400 individuals and 5 variables: id, y.repeated, y.trend, time and sex.</dd> <dt>GRM</dt>
<dd>a genetic relationship matrix for 400 observations.</dd> 
</dl>

Format

Example dataset — example

Contains the following objects:<dl>
 <dt>pheno</dt>
<dd>a data frame of 400 observations from a cross-sectional study with 5 variables: id, disease, trait, age and sex.</dd>

 <dt>pheno2</dt>
<dd>a data frame of 2,000 observations from a longitudinal study with 400 individuals and 5 variables: id, y.repeated, y.trend, time and sex.</dd>

 <dt>GRM</dt>
<dd>a genetic relationship matrix for 400 observations.</dd>

 
</dl>

Example dataset

example: Example dataset

Description

Arguments

Format