GWAF (version 2.2)

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

Description

Fit linear mixed effects (LME) model to test associations between a continuous phenotype and all imputed SNPs in a genotype file in family data under additive 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 from package coxme is used.

Usage

lmepack.batch.imputed(phenfile, genfile, pedfile, phen, kinmat, covars = NULL, 
outfile, col.names = T, sep.ped = ",", sep.phe = ",", sep.gen = ",")

Arguments

phenfile

a character string naming the phenotype file for reading (see format requirement in details)

genfile

a character string naming the genotype file for reading (see format requirement in details)

pedfile

a character string naming the pedigree file for reading (see format requirement in details)

phen

a character string for a phenotype name in phenfile

kinmat

a character string naming the file where kinship coefficient matrix is kept

covars

a character vector for covariates in phenfile

outfile

a character string naming the result file for writing

col.names

a logical value indicating whether the output file should contain column names

sep.ped

the field separator character for pedigree file

sep.phe

the field separator character for phenotype file

sep.gen

the field separator character for genotype file

Value

No value is returned. Instead, results are written to outfile.

phen

phenotype name

snp

SNP name

N

the number of individuals in analysis

AF

imputed allele frequency of coded allele

h2q

the portion of phenotypic variation explained by the SNP

beta

regression coefficient of SNP covariate

se

standard error of beta

pval

p-value of testing beta not equal to zero

Details

Similar to the details for lmepack.batch function but here the SNP data contains imputed genotypes (allele dosages) that are continuous and range from 0 to 2. In addition, the user specified genetic model argument is not available.

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. Association analysis in a variance components framework. Genet Epidemiol, 21 Suppl 1, S341-S346 (2001).

Examples

## Not run: 
# lmepack.batch.imputed(phenfile="simphen.csv",genfile="simgen.csv",pedfile="simped.csv",
# phen="SIMQT",kinmat="simkmat.Rdata",outfile="simout.csv",covars=c("age","sex"),
# sep.ped=",",sep.phe=",",sep.gen=",")
# ## End(Not run)