summary.snpClogit {SimHap} | R Documentation |
Summary method for objects of class snpClogit
## 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"), ...)
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. |
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. |
Pamela A. McCaskie
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.
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)