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

Description

Fit linear mixed effects (LME) model to test association between a continuous phenotype and all SNPs in a genotype file in family data under user specified 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 As kinship package has been archived, GWAF package now includes functions from kinship package to support the modified lmekin function.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(phenfile, genfile, pedfile, phen, kinmat, model = "a", covars = NULL, 
outfile, col.names = T, sep.ped = ",", sep.phe = ",", sep.gen = ",")

Arguments

Value

No value is returned. Instead, results are written to outfile. When the genetic model is 'a', 'd' or 'r', the result includes the following columns. When the genetic model is 'g', beta and se are replaced with beta10, beta20, beta21, se10, se20, se21.phenphenotype namesnpSNP namen0the number of individuals with 0 copy of coded allelesn1the number of individuals with 1 copy of coded allelesn2the number of individuals with 2 copies of coded allelesh2qthe portion of phenotypic variation explained by the SNPbetaregression coefficient of SNP covariatesestandard error of betachisqChi-square statistic for testing beta not equal to zerodfdegree of freedom of the Chi-square statisticmodelmodel actually used in the analysispvalp-value of the chi-square statisticbeta10regression coefficient of genotype with 1 copy of coded allele vs. that with 0 copybeta20regression coefficient of genotype with 2 copy of coded allele vs. that with 0 copybeta21regression coefficient of genotype with 2 copy of coded allele vs. that with 1 copyse10standard error of beta10se20standard error of beta20se21standard error of beta21

Details

The lmepack.batch function first reads in and merges phenotype-covariates, genotype and pedigree files, then tests the association of phen against all SNPs in genfile. genfile contains unique individual id and genotype data, with the column names being "id" and SNP names. For each SNP, the genotype data should be coded as 0, 1, 2 indicating the numbers of the coded alleles. The SNP name in genotype file should not have any dash, '-' and other special characters(dots and underscores are OK). phenfile contains unique individual id, phenotype and covariates data, with the column names being "id" and phenotype and covaraite names. pedfile contains pedigree informaion, with the column names being "famid","id","fa","mo","sex". In all files, missing value should be an empty space, except missing parental id in pedfile. SNPs with low genotype counts (especially minor allele homozygote) may be omitted or analyzed with dominant model. The lmepack.batch function fits LME model using a modified lmekin function from kinship package.

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).