geepack.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 logistic regression via GEE 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, 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 geepack. This function is called in geepack.lgst.batch function to apply association test to all SNPs in the genotype data.

Usage

geepack.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 geepack.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 geepack.lgst.batch.

Author(s)

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

References

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.

See Also

geese function from package geepack

Examples

## Not run: 
geepack.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.