lmepack.batch.imputed: function to test associations between a continuous trait and a batch of imputed SNPs in families using Linear Mixed Effects model

Description

Fit linear mixed effects (LME) model to test associations between a continuous phenotype and all imputed SNPs in a genotype file in family data under additive genetic model. The SNP genotype is treated as a fixed effect, and a random effect correlated according to degree of relatedness within a family is also fitted. In each trait-SNP assocaition test, 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 As kinship package has been archived, GWAF package now includes functions from kinship package to support the modified lmekin function.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.batch.imputed(phenfile, genfile, pedfile, phen, kinmat, covars = NULL, 
outfile, col.names = T, sep.ped = ",", sep.phe = ",", sep.gen = ",")

Arguments

Value

No value is returned. Instead, results are written to outfile.phenphenotype namesnpSNP nameNthe number of individuals in analysisAFimputed allele frequency of coded alleleh2qthe portion of phenotypic variation explained by the SNPbetaregression coefficient of SNP covariatesestandard error of betapvalp-value of testing beta not equal to zero

Details

Similar to the details for lmepack.batch 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.

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).