lme.batch.imputed {GWAF}R Documentation

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 model to test association between a continuous phenotype and all imputed SNPs in a genotype file. The SNP genotype is treated as fixed effects, 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 which is modified from the same named function in package kinship is used.

Usage

lme.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

Details

Similar to the details for lme.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.

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 the chi-square statistic

Author(s)

Qiong Yang <qyang@bu.edu> and Ming-Huei Chen <mhchen@bu.edu>

References

kinship 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/.

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).


[Package GWAF version 1.2 Index]