summary.hapBin {SimHap}R Documentation

Summarize binary haplotype analysis models

Description

Summary method for objects of class hapBin

Usage

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

Arguments

object object of class hapBin, the result of a call to haplo.bin.
x an object of class summary.hapBin, the result of a call to
summary.hapBin.
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

formula formula1 passed into haplo.bin.
coefficients a table containing the odds ratios, confidence intervals and p-values of the parameter estimates.
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.
empiricalResults a list containing the odds ratios, confidence intervals and p-values calculated at each simulation of haplo.bin.
effect the haplotypic effect modelled: `ADDITIVE', `DOMINANT' or `RECESSIVE'.

Note

See help for haplo.bin for more details.

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.bin(formula1=PLAQUE~AGE+SBP+h.N1AA, 
        formula2=PLAQUE~AGE+SBP, pheno=pheno.dat, haplo=myhaplo, 
        sim=10)


[Package SimHap version 1.0.0 Index]