GWAF (version 2.2)

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

Description

Fit linear mixed effects (LME) model to test associations between a continuous phenotype and all SNPs in a genotype file in family data under user specified 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(phenfile, genfile, pedfile, phen, kinmat, model = "a", covars = NULL, 
outfile, col.names = T, sep.ped = ",", sep.phe = ",", sep.gen = ",")

Arguments

genfile

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

phenfile

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

pedfile

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

outfile

a character string naming the result file for writing

phen

a character string for a phenotype name in phenfile

covars

a character vector for covariates in phenfile

model

a single character of 'a','d','g', or 'r', with 'a'=additive, 'd'=dominant, 'g'=general and 'r'=recessive models

kinmat

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

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. When the genetic model is 'a', 'd' or 'r', the result includes the following columns. When the genetic model is 'g', beta and se are replaced with beta10, beta20, beta21, se10, se20, se21.

phen

phenotype name

snp

SNP name

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

h2q

the portion of phenotypic variation explained by the SNP

beta

regression coefficient of SNP covariate

se

standard error of beta

chisq

Chi-square statistic for testing beta not equal to zero

df

degree of freedom of the Chi-square statistic

model

model actually used in the analysis

pval

p-value of the chi-square statistic

beta10

regression coefficient of genotype with 1 copy of coded allele vs. that with 0 copy

beta20

regression coefficient of genotype with 2 copy of coded allele vs. that with 0 copy

beta21

regression coefficient of genotype with 2 copy of coded allele vs. that with 1 copy

se10

standard error of beta10

se20

standard error of beta20

se21

standard error of beta21

Details

The lmepack.batch function first reads in and merges phenotype-covariates, genotype and pedigree files, then tests the association of phen against all SNPs in genfile. genfile contains unique individual id and genotype data, with the column names being "id" and SNP names. For each SNP, the genotype data should be coded as 0, 1, 2 indicating the numbers of the coded alleles. The SNP name in genotype file should not have any dash, '-' and other special characters(dots and underscores are OK). phenfile contains unique individual id, phenotype and covariates data, with the column names being "id" and phenotype and covaraite names. pedfile contains pedigree informaion, with the column names being "famid","id","fa","mo","sex". In all files, missing value should be an empty space, except missing parental id in pedfile. SNPs with low genotype counts (especially minor allele homozygote) may be omitted or analyzed with dominant model. The lmepack.batch function fits LME model using a modified lmekin function from coxme package.

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 Programhttp://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(phenfile="simphen.csv",genfile="simgen.csv",pedfile="simped.csv",
# phen="SIMQT",kinmat="simkmat.Rdata",model="a",outfile="simout.csv",col.names=T,
# sep.ped=",",sep.phe=",",sep.gen=",")
# ## End(Not run)