R: A likelihood ratio test of population Hardy-Weinberg...

hwe.cc {gap} | R Documentation

## 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

`model` | model specification, dominant, recessive
`case` | a vector of genotype counts in cases
`ctrl` | a vector of genotype counts in controls
`k0` | prevalence of disease in the population
`initial1` | initial values for beta, gamma, and q
`initial2` | initial values for logit(p) and log(gamma)

### 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.

`Cox` | statistics under a general model
`t2par` | under the null hypothesis
`t3par` | under the alternative hypothesis
`lrt.stat` | the log-likelihood ratio statistic
`pval` | the corresponding p value

### 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)

[Package gap version 1.2.2 Index]