lmepack.int.batch.imputed: function to test gene-environment or gene-gen interaction and associations between a continuous trait and a batch of imputed SNPs in families using Linear Mixed Effects model

Description

Fit linear mixed effect model to test gene-environment or gene-gen interaction and genetic association for a continuous phenotype and all imputed SNPs in a genotype file under additive genetic model. The interaction term is the product of SNP genotype (allelic dosage) and a covariate for interaction (cov.int). The covariate for interaction (cov.int) can be SNP genotype (gene-gene interaction) or an environmental factor (gene-environment interaction). Only one interaction term is allowed. When (cov.int) is dichotomous, stratified analyses can be requested by specifying sub="Y". The covariance between the main effect (SNP) and the interaction effect is provided in the output when stratified analysis is not requested. The SNP genotype and the interaction are treated as fixed effectd, and a random effect correlated according to degree of relatedness within a family is also fitted. In each test for trait-SNP assocaition or interaction, the lmekin() function which is modified from the same named function in package kinship is used. As kinship package has been archived, GWAF package now includes functions from kinship package to support the modified lmekin function. Archived kinship package can be found at http://cran.r-project.org/web/packages/kinship/index.html.

Usage

lmepack.int.batch.imputed(phenfile,genfile,pedfile,phen,kinmat,covars,cov.int,sub="N",
outfile,col.names=T,sep.ped=",",sep.phe=",",sep.gen=",")

Arguments

Value

Please see value in 'lmepack.int.batch' function.

Details

Similar to the details for 'lmepack.int.batch' function but here the SNP data contains imputed genotypes (allele dosages) that are continuous and range from 0 to 2.

References

kinship package: mixed-effects Cox models, sparse matrices, and modeling data from large pedigrees. Beth Atkinson (atkinson@mayo.edu) for pedigree functions.Terry Therneau (therneau@mayo.edu) for all other functions. 2007. Ref Type: Computer Program http://cran.r-project.org/.

Abecasis, G. R., Cardon, L. R., Cookson, W. O., Sham, P. C., & Cherny, S. S. Association analysis in a variance components framework. Genet Epidemiol, 21 Suppl 1, S341-S346 (2001).