geepack.lgst.batch.imputed: function to test genetic associations between a dichotomous...

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

Description

Fit logistic regression via Generalized Estimation Equation (GEE) to test associations between a dichotomous phenotype and all imputed SNPs in a genotype file in family data under additive genetic model. Each family is treated as a cluster, with independence working correlation matrix used in the robust variance estimator. This function applies the same trait-SNP association test to all SNPs in the imputed genotype data. The trait-SNP association test is carried out by geepack.lgst.imputed function where the geese function from package geepack is used.

Usage

geepack.lgst.batch.imputed(genfile, phenfile, pedfile, outfile, phen, 
covars = NULL, 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
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 geepack.lgst.batch 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
Nd	the number of individuals in affected sample in analysis
AF	imputed allele frequency of coded allele
AFd	imputed allele frequency of coded allele in affected sample
beta	regression coefficient of SNP covariate
se	standard error of beta
remark	warning or additional information for the analysis, note that the genotype counts are based on rounded imputed genotypes; 'not converged' indicates the GEE analysis did not converge; 'logistic reg' indicates GEE model is replaced by logistic regression; 'exp count<5' indicates any expected count is less than 5 in phenotype-genotype table; 'not converged and exp count<5', 'logistic reg & exp count<5' are noted similarly; 'collinearity' indicates collinearity exists between SNP and some covariates
pval	p-value of the association test based on chi-square statistic

Author(s)

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

Examples

## Not run: 
geepack.lgst.batch.imputed(phenfile="simphen.csv",genfile="simgen.csv",
pedfile="simped.csv",phen="aff",covars="sex",outfile="simout.csv",col.names=T,
sep.ped=",",sep.phe=",",sep.gen=",")

## End(Not run)

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