glmm.lgst: function for testing association between a dichotomous trait...

In GWAF: Genome-Wide Association/Interaction Analysis and Rare Variant Analysis with Family Data

Description

Fit a Generalized Linear Mixed Effects model (GLMM) with logistic link and a normal distributed random intercept for each cluster to test association between a dichotomous phenotype and one genotyped SNP in a genotype file with user specified genetic model. Each family is treated as a cluster. When analyze rare variants for dichotomous traits, GLMM, as implemeted by this function, is recommended over other methods such as GEE. The trait-SNP association test is carried out by the lmer function from package lme4. This function is called in glmm.lgst.batch function to apply association test to all SNPs in the genotype data.

Usage

glmm.lgst(snp, phen, test.dat, covar = NULL, model = "a")

Arguments

snp	genotype data of a SNP
phen	a character string for a phenotype name in test.dat
test.dat	the product of merging phenotype, genotype and pedigree data, should be ordered by "famid"
covar	a character vector for covariates in test.dat
model	a single character of 'a','d','g', or 'r', with 'a'=additive, 'd'=dominant, 'g'=general and 'r'=recessive models

Details

The glmm.lgst function tests association between a dichtomous trait and a SNP from a dataset that contains phenotype, genotype and pedigree data (test.dat), where the dataset needs to be ordered by famid.

Value

Please see output in glmm.lgst.batch.

Author(s)

Qiong Yang <[e-mail]> and Ming-Huei Chen <[e-mail]>

References

Bates D, Maechler M and Bolker B. (2010) lme4: Linear mixed-effects models using S4 classes Longitudinal data analysis using generalized linear models. http://cran.r-project.org/web/packages/lme4/.

Chen MH, Liu X, Wei F, Larson MG, Fox CS, Vasan RS and Yang Q. (2011) A comparison of strategies for analyzing dichotomous outcomes in genome-wide association studies with general pedigrees. Genetic Epidemiology 35:650-657.

See Also

lmer function from package lme4

Examples

## Not run: 
glmm.lgst(snp=data[,"rs123"],phen="CVD",test.dat=data,model="a",covar=c("age","sex"))

## End(Not run)

GWAF documentation built on May 2, 2019, 2:47 p.m.