summary.snpClogit {SimHap}R Documentation

Summarizing Single SNP analysis models for matched case-control data

Description

Summary method for objects of class snpClogit

Usage

## S3 method for class 'snpClogit':
summary(object, ...)
## S3 method for class 'summary.snpClogit':
print(x, digits = max(3, getOption("digits") - 3), 
        signif.stars = getOption("show.signif.stars"), ...)

Arguments

object an object of class snpClogit
x an object of class summary.snpClogit, the result of a call to
summary.snpClogit.
digits the number of significant digits to use when printing.
signif.stars logical. If TRUE, ``significance stars" are printed for each coefficient.
... further arguments passed to or from other methods.

Value

summary.snpClogit returns an object of class summary.snpClogit, a list with components

terms terms attribute of formula1 called in snp.cc.match.
coefficients summarized results from fitted model, including odds ratios and p-values.
formula formula1 used in snp.cc.match.
LRT likelihood ratio test comparing the model with SNP variables compared to the model without SNPs.
Wald Wald statistic for the fitted model.
rsquared adjusted r-squared values for the fitted model.
residuals the residuals, that is response minus fitted values.

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.cc.match

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)


[Package SimHap version 1.0.0 Index]