lme.EC: function for testing a single/pooled variant for continuous traits with family data using Linear Mixed Effects model

Description

Fit linear mixed effects (LME) model to test a single/pooled variant for associations against a continuous phenotype with family data. The lmekin function from package coxme is used.

Usage

lme.EC(snp,phen,test.dat,covar,kmat,chr)

Arguments

snp

a numeric vector with genotype of a single/pooled variant

phen

a character string for the phenotype name of a continuous trait of interest in test.dat

test.dat

the product of merging phenotype, genotype and pedigree data

covar

a character vector for covariates in test.dat

kmat

relationship coefficient (twice of kinship coefficient) matrix based on pedigree file

chr

chromosome number

Value

ntotal: number of individuals with genotype, phenotype and covariates
nmiss: number of individuals with missing genotype among ntotal
maf_ntotal: minor allele frequency based on ntotal
beta: regression coefficient of single SNP test or burden test
se: standard error of beta
Z: Wald Z statistic
remark: additional information of the analysis
p: p-value of single SNP test or burden test
MAC: minor allele count
n0: the number of individuals with 0 copy of coded alleles
n1: the number of individuals with 1 copy of coded alleles
n2: the number of individuals with 2 copies of coded alleles

Details

The lme.EC function fits a Linear Mixed Effects model (LME) that uses relationship coefficient matrix as within pedigree correlation matrix to test association between a continuous phenotype and a single/pooled genetic variant with additive model. The trait-SNP association test is carried out by the lmekin function from package coxme. This function is called in lme.ped function to test all single/pooled variants.

References

coxme 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/web/packages/coxme/.

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

Examples

Run this code

## Not run: 
# lme.EC(snp=rsnps.dat$counts,phen="trait",test.dat=rsnps.dat,
# covar=c("age","sex"),kmat=kmat,chr=1)## End(Not run)

Run the code above in your browser using DataLab