Fit logistic regression via Generalized Estimation Equation (GEE) to test association between a dichotomous phenotype
and one imputed SNP in a genotype file in family data under additive genetic model. Each family is treated as
a cluster, with independence working correlation matrix used in the robust variance estimator. The trait-SNP association
test is carried out by the
geese function from package
This function is called in
geepack.lgst.batch.imputed function to apply association test to all imputed SNPs in a
imputed genotype data of a SNP
a character string for a phenotype name in
the product of merging phenotype, genotype and pedigree data, should be ordered by "famid"
a character vector for covariates in
Similar to the details for
geepack.lgst function but here the SNP data contains imputed genotypes (allele dosages)
that are continuous and range from 0 to 2. In addition, the user-specified genetic model argument is not available.
Please see output in
Qiong Yang <email@example.com> and Ming-Huei Chen <firstname.lastname@example.org>
Liang, K.Y. and Zeger, S.L. (1986) Longitudinal data analysis using generalized linear models. Biometrika, 73 13–22.
Zeger, S.L. and Liang, K.Y. (1986) Longitudinal data analysis for discrete and continuous outcomes. Biometrics, 42 121–130.
Yan, J and Fine, J. (2004) Estimating equations for association structures. Stat Med, 23 859–874.
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