lmeV.batch.imputed: function to efficiently test associations between a...

In GWAF: Genome-Wide Association/Interaction Analysis and Rare Variant Analysis with Family Data

Description

A faster version of function lmepack.batch.imputed. Unlike lmepack.batch.imputed that estimates polygenic variation for every SNP in a batch of imputed SNPs, lmeVpack.batch.imputed only estimates once for a batch of imputed SNPs. Particularly recommended for analyzing 1000G imputed genotype data.

Usage

lmeVpack.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 lmepack.batch.imputed.

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

Author(s)

Qiong Yang <[e-mail]> and Ming-Huei Chen <[e-mail]>

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/.

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: 
lmeVpack.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)

GWAF documentation built on May 2, 2019, 2:47 p.m.