summary.hapQuant {SimHap}R Documentation

Summarize quantitative haplotype analysis models

Description

Summary method for objects of class hapQuant

Usage

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

Arguments

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

formula formula1 passed into haplo.quant.
coefficients a table containing the coefficients, standard errors and p-values of the parameter estimates.
empiricalResults a list containing the coefficients, standard errors and p-values calculated at each simulation of haplo.quant.
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.
AIC Akaike Information Criterion for the linear model fit including haplotypes.
predicted estimated marginal means of the outcome variable broken down by haplotype levels, evaluated at mean values of the model predictors, averaged over all simulations.
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.quant

Examples


data(SNP.dat)

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

data(pheno.dat)

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

# print haplotype frequencies generated by infer.haplos
myinfer$hap.freq 

# generate haplo object where haplotypes with a frequency 
# below min.freq are grouped as a category called "rare"
myhaplo<-make.haplo.rare(myinfer,min.freq=0.05) 
mymodel <- haplo.quant(formula1=HDL~AGE+SBP+h.N1AA, formula2=HDL~AGE+SBP, 
        pheno=pheno.dat, haplo=myhaplo, sim=10)
summary(mymodel)


[Package SimHap version 1.0.0 Index]