snp.cc.match {SimHap}R Documentation

Single SNP analysis for matched case-control data

Description

snp.cc.match is used to fit conditional logistic regression models to single SNP genotype and phenotype, matched case-control data.

Usage

snp.cc.match(formula1, formula2, geno, pheno, sub = NULL)

Arguments

formula1 a symbolic description of the full model to be fit, including SNP parameters. The response must be binary indicator of case-control status, and the formula must contain a variable indicating strata, or the matching sequence.
formula2 a symbolic description of the nested model excluding SNP parameters, to be compared to formula1 in a likelihood ratio test. The response must be binary indicator of case-control status, and the formula must contain a variable indicating strata, or the matching sequence.
geno a dataframe containing genotype data.
pheno a dataframe containing phenotype data.
sub an expression representing a subset of the data on which to perform the models.

Details

formula1 should be in the form:

response ~ predictor(s) + strata(strata_variable) + SNP(s)
and formula2 should be in the form:
response ~ predictor(s) + strata(strata_variable).
If case-control data is not matched, the snp.bin function should be used.

Value

snp.Clogit returns an object of class snpClogit.
The summary function can be used to obtain and print a summary of the results.
An object of class snpClogit is a list containing the following components:

results a table containing the hazard ratios, confidence intervals and p-values of the parameter estimates.
formula formula1 passed to snp.cc.match.
Wald The Wald test for overall significance of the fitted model.
logLik the log-likelihood for the model fit using formula1.
fit.clogit an object of class clogit fit using formula1. See clogit for details.
rsquared r-squared values for models fit using formula1 and formula2.

Author(s)

Pamela A. McCaskie

References

McCaskie, P.A., Carter, K.W. Hazelton, M., Palmer, L.J. (2007) SimHap: A comprehensive modeling framework for epidemiological outcomes and a multiple-imputation approach to haplotypic analysis of population-based data, [online] www.genepi.org.au/simhap.

See Also

snp.bin

Examples


data(SNP.dat)

# convert SNP.dat to format required by snp.cc.match
geno.dat <- SNP2Geno(SNP.dat, baseline=c("MM", "11", "GG", "CC"))

data(pheno.dat)
mymodel <- snp.cc.match(formula1=DISEASE~SBP+DBP+SNP_1_add+strata(STRAT), 
        formula2=DISEASE~SBP+DBP+strata(STRAT), pheno=pheno.dat, 
        geno=geno.dat)
summary(mymodel)

# example with subsetting variable
mymodel <- snp.cc.match(formula1=DISEASE~SBP+DBP+SNP_1_add+strata(STRAT), 
        formula2=DISEASE~SBP+DBP+strata(STRAT), pheno=pheno.dat, 
        geno=geno.dat, sub=expression(SEX==1))
summary(mymodel)

[Package SimHap version 1.0.0 Index]