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)