gee.lgst.imputed {GWAF} | R Documentation |
Fit logistic regression via GEE to test association between a dichotomous phenotype and one imputed SNP in a genotype file. Each family is treated as a cluster, with independence working correlation matrix used in the robust variance estimator. This function is called in gee.lgst.batch.imputed function to apply association test to all imputed SNPs in the genotype data.
gee.lgst.imputed(snp, phen, test.dat, covar = NULL)
snp |
imputed genotype data of a SNP |
phen |
a character string for a phenotype name in phenfile |
test.dat |
the product of merging phenotype, genotype and pedigree data, should be ordered by "famid" |
covar |
a character vector for covariates in phenfile |
Similar to the details for 'gee.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 gee.lgst.batch.imputed.R.
Qiong Yang <qyang@bu.edu> and Ming-Huei Chen <mhchen@bu.edu>
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.
Vincent J Carey.Ported to R by Thomas Lumley (versions 3.13 and 4.4) and Brian Ripley (version 4.13). gee: Generalized Estimation Equation solver. [4.13]. 2007. Ref Type: Computer Program, http://cran.r-project.org/
gee()
function from package gee