summary.hapSurv {SimHap}R Documentation

Summarize haplotype analysis models for survival data

Description

Summary method for objects of class hapSurv

Usage

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

Arguments

object an object of class hapSurv, a result of a call to haplo.surv.
x an object of class summary.hapSurv, the result of a call to
summary.hapSurv.
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.hapSurv returns an object of class summary.hapSurv, a list with components

formula formula1 passed into haplo.surv.
coefficients summarized results from fitted model, including hazard ratios and p-values.
empiricalResults a list containing the hazard ratios, confidence intervals and p-values calculated at each simulation of haplo.surv.
rsquared r-squared values for the model including haplotypes and the model excluding haplotypes.
LRT a likelihood ratio test, testing for significant improvement of the model when haplotypic parameters are included.
Wald The Wald test for overall significance of the fitted model.
effect the haplotypic effect modelled: `ADDITIVE', `DOMINANT' or `RECESSIVE'.

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

haplo.surv

Examples


data(SNPsurv.dat)

# convert SNP.dat to format required by infer.haplos
survHaplo.dat <- SNP2Haplo(SNPsurv.dat)

data(survPheno.dat)

# generate haplotype frequencies and haplotype design matrix
myinfer<-infer.haplos(survHaplo.dat) 

# print haplotype frequencies generated by infer.haplos
myinfer$hap.freq 
myhaplo<-make.haplo.rare(myinfer,min.freq=0.05)
mymodel <- haplo.surv(formula1=Surv(time, status)~age+h.V1AA, 
        formula2=Surv(time, status)~age, haplo=myhaplo, 
        pheno=survPheno.dat, sim=10)
summary(mymodel)


[Package SimHap version 1.0.0 Index]