GWAF (version 2.2)

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 interactions and genetic associations 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 from package coxme is used.

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

phenfile

a character string naming the phenotype file for reading (see format requirement in details)

genfile

a character string naming the (imputed) genotype file for reading (see format requirement in details)

pedfile

a character string naming the pedigree file for reading (see format requirement in details)

outfile

a character string naming the result file for writing

phen

a character string for a phenotype name in phenfile

covars

a character vector for covariates in phenfile

cov.int

a character string naming the covariate for interaction, the covariate has to be included in covars

sub

"N" (default) for no stratified analysis, and "Y" for requesting stratified analyses (only when cov.int is dichotomous)

kinmat

a character string naming the file where kinship coefficient matrix is kept

col.names

a logical value indicating whether the output file should contain column names

sep.ped

the field separator character for pedigree file

sep.phe

the field separator character for phenotype file

sep.gen

the field separator character for genotype file

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

coxme package: mixed-effects Cox models, sparse matrices, and modeling data from large pedigrees. Beth Atkinson ([e-mail]) for pedigree functions.Terry Therneau ([e-mail]) 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).

Examples

## Not run: 
# lmepack.int.batch.imputed(phenfile="simphen.csv",genfile="simgen.csv",pedfile="simped.csv",
# phen="SIMQT",kinmat="simkmat.Rdata",outfile="simout.csv",covars=c("age","sex"),
# cov.int="sex",sub="Y",sep.ped=",",sep.phe=",",sep.gen=",")
# ## End(Not run)