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

In RVFam: Rare Variants Association Analyses with Family Data

Description

Fit generalized linear mixed effects model (GLMM) with logistic link that treats each pedigree as a cluster to test a single/pooled variant for associations against a continuous phenotype with family data. The glmer function from package lme4 is used.

Usage

glmm.EC(snp,phen,test.dat,covar,chr)

Arguments

snp	a numeric vector with genotype of a single/pooled variant
phen	a character string for the phenotype name of a binary trait of interest in test.dat
test.dat	the product of merging phenotype, genotype and pedigree data, should be ordered by "famid"
covar	a character vector for covariates in test.dat
chr	chromosome number

Details

The glmm.EC function fits a generalized linear mixed effects model (GLMM) with logistic link that treats each pedigree as a cluster to test association between a binary trait and a single/pooled genetic variant with additive model. The trait-variant association test is carried out by the glmer function from package lme4. P-value from likelihood ratio test (LRT) is reported. This function is called in glmm.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	Z statistic based on signed LRT
remark	additional information of the analysis
p	LRT p-value of a single variant 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

Bates D, Maechler M, Bolker B and Walker S (2014). lme4: Linear mixed-effects models using Eigen and S4. R package version 1.1-7, http://CRAN.R-project.org/package=lme4.

Examples

## Not run: 
glmm.EC(snp=rsnps.dat[,"snp1"],phen="disease",test.dat=rsnps.dat,
covar=c("sex"),chr=1)

## End(Not run)

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