data(lucaDat)
# typical penetrance model:
pen.model<-formula(d~I(allele.count(g,"C"))+a+a2+I(allele.count(g,"C")):a)
#1. Assuming independence and HWP
fitHWP<-luca(pen.model=pen.model, gLabel="g", dat=lucaDat, HWP=TRUE)
fitHWP$coef
fitHWP$var
summary.luca(fitHWP) # OR 'summary(fitHWP)'
#2. Assuming independence only
fitDefault<-luca(pen.model=pen.model, gLabel="g", dat=lucaDat)
fitDefault$coef
fitDefault$var
#3. Allowing for dependence between genetic and nongenetic factors
# General dependence model
fitDep1<-luca(pen.model=pen.model, gLabel="g", dat=lucaDat,
dep.model=formula(g~a))
fitDep1$coef
fitDep1$var
# When 'g' and 'a' are conditioanally independent given the third variable 'a2':
fitDep2<-luca(pen.model=pen.model, gLabel="g", dat=lucaDat,
dep.model=formula(g~a2))
fitDep2$coef
fitDep2$var
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