hwe {gap}R Documentation

Hardy-Weinberg equlibrium test for a multiallelic marker

Description

Hardy-Weinberg equilibrium test

Usage

hwe(data, data.type="allele", yates.correct=FALSE, miss.val=0)

Arguments

data A rectangular data containing the genotype, or an array of genotype counts
data.type An option taking values "allele", "genotype", "count" if data is alleles, genotype or genotype count
yates.correct A flag indicating if Yates' correction is used for Pearson chi-squared statistic
miss.val A list of missing values

Details

This function obtains Hardy-Weinberg equilibrium test statistics. It can handle data coded as allele numbers (default), genotype identifiers (by setting data.type="genotype") and counts corresponding to individual genotypes (by setting data.type="count") which requires that genotype counts for all n(n+1) possible genotypes, with n being the number of alleles.

For highly polymorphic markers when asymptotic results do not hold, please resort to hwe.hardy.

Value

The returned value is a list containing:

allele.freq Frequencies of alleles
x2 Pearson chi-square
p.x2 p value for chi-square
lrt Log-likelihood ratio test statistic
p.lrt p value for lrt
df Degree(s) of freedom
rho sqrt{chi-square/N} the contingency table coefficient

Author(s)

Jing Hua Zhao

See Also

hwe.hardy

Examples

## Not run: 
data(hla)
hla.DQR <- hwe(hla[,3:4])
summary(hla.DQR)
a <- c(3,2,2)
a.out <- hwe(a,data.type="genotype")
a.out
a.out <- hwe(a,data.type="count")
a.out
## End(Not run)

[Package gap version 1.0-17 Index]