| summary.hapQuant {SimHap} | R Documentation |
Summary method for objects of class hapQuant
## 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"), ...)
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. |
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'. |
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 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)