Description Usage Arguments Details Value Author(s) References Examples
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.
1 | lme.EC(snp,phen,test.dat,covar,kmat,chr)
|
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 |
the product of merging phenotype, genotype and pedigree data |
covar |
a character vector for covariates in |
kmat |
relationship coefficient (twice of kinship coefficient) matrix based on pedigree file |
chr |
chromosome number |
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.
ntotal |
number of individuals with genotype, phenotype and covariates |
nmiss |
number of individuals with missing genotype among |
maf_ntotal |
minor allele frequency based on |
beta |
regression coefficient of single SNP test or burden test |
se |
standard error of |
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 |
Ming-Huei Chen <mhchen@bu.edu> and Qiong Yang <qyang@bu.edu>
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.
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