hwe.cc: A likelihood ratio test of population Hardy-Weinberg...

In gap: Genetic Analysis Package

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

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

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.

Author(s)

Chang Yu, Li Wang, Jing Hua Zhao

References

\insertRef

yu09gap

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)

gap documentation built on Aug. 26, 2023, 5:07 p.m.