summary.snpSurv {SimHap} | R Documentation |
Summary method for objects of class snpSurv
## S3 method for class 'snpSurv': summary(object, ...) ## S3 method for class 'summary.snpSurv': print(x, digits = max(3, getOption("digits") - 3), signif.stars = getOption("show.signif.stars"), ...)
object |
an object of class snpSurv |
x |
an object of class summary.snpSurv , the result of a call to summary.snpSurv. |
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.snpSurv
returns an object of class summary.snpSurv
, a list with components
terms |
terms attribute of formula1 called in snp.surv . |
coefficients |
summarized results from fitted model, including hazard ratios and p-values. |
formula |
formula1 used in snp.surv . |
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(SNPsurv.dat) # transforms SNPlong.dat to an object containing 3 columns # per SNP - additive, dominant and recessive, where genotypes # defined in 'baseline' serve as the baseline genotypes survGeno.dat <- SNP2Geno(SNPsurv.dat, baseline=c("V2V2", "GG", "CC")) data(survPheno.dat) mymodel <- snp.surv(formula1=Surv(time, status)~age+SNP_1_add, formula2=Surv(time, status)~age, pheno=survPheno.dat, geno=survGeno.dat) summary(mymodel)