A likelihood ratio test of population Hardy-Weinberg equilibrium for case-control studies

Description

A likelihood ratio test of population Hardy-Weinberg equilibrium for case-control studies

Usage

hwe.cc(model, case, ctrl, k0, initial1, initial2)

Arguments

Details

This is a collection of utility functions. The null hypothesis declares that the proportions of genotypes are according to Hardy-Weinberg law, while under the alternative hypothesis, the expected genotype counts are according to the probabilities that particular genotypes are obtained conditional on the prevalence of disease in the population. In so doing, Hardy-Weinberg equilibrium is considered using both case and control samples but pending on the disease model such that 2-parameter multiplicative model is built on baseline genotype alpha, alpha beta and alpha gamma.

Value

The returned value is a list with the following components.

References

Yu C, Zhang S, Zhou C, Sile S. A likelihood ratio test of population Hardy-Weinberg equilibrium for case-control studies. Genetic Epidemiology 33:275-280, 2009

Author(s)

Chang Yu, http://biostat.mc.vanderbilt.edu/wiki/Main/ChangYu, Li Wang, Jing Hua Zhao

See Also

hwe

Examples

## Not run: 

### Saba Sile, email of Jan 26, 2007, data always in order of GG AG AA, p=Pr(G),
### q=1-p=Pr(A)
case=c(155,27,4)
ctrl=c(408,55,15)
k0=.2
initial1=c(1.0,0.94,0.0904)
initial2=c(logit(1-0.0904),log(0.94))
hwe.cc("recessive",case,ctrl,k0, initial1, initial2)

### John Phillips III, TGFb1 data codon 10: TT CT CC, CC is abnormal and increasing
### TGFb1 activity
case=c(29,78,13)
ctrl=c(17,28,6)
k0 <- 1e-5
initial1 <- c(2.45,2.45,0.34)
initial2 <- c(logit(1-0.34),log(2.45))
hwe.cc("dominant",case,ctrl,k0,initial1,initial2)

## End(Not run)

Results