lme.EC: function for testing a single/pooled variant for continuous...

In RVFam: Rare Variants Association Analyses with Family Data

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

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.

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

Author(s)

Ming-Huei Chen <[e-mail]> and Qiong Yang <[e-mail]>

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/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

## 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)

RVFam documentation built on May 2, 2019, 8:26 a.m.