hwe: Hardy-Weinberg equlibrium test for a multiallelic marker

In gap: Genetic Analysis Package

Hardy-Weinberg equlibrium test for a multiallelic marker

Description

Hardy-Weinberg equlibrium test for a multiallelic marker

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^2 statistic.
miss.val	A list of missing values.

Details

Hardy-Weinberg equilibrium test.

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^2.

• p.x2 p value for \chi^2.

• lrt Log-likelihood ratio test statistic.

• p.lrt p value for lrt.

• df Degree(s) of freedom.

• rho \sqrt{\chi^2/N} the contingency table coefficient.

Author(s)

Jing Hua Zhao

See Also

hwe.hardy

Examples

## Not run: 
a <- c(3,2,2)
a.out <- hwe(a,data.type="genotype")
a.out
a.out <- hwe(a,data.type="count")
a.out
require(haplo.stats)
data(hla)
hla.DQR <- hwe(hla[,3:4])
summary(hla.DQR)
# multiple markers
s <- vector()
for(i in seq(3,8,2))
{
  hwe_i <- hwe(hla[,i:(i+1)])
  s <- rbind(s,hwe_i)
}
s

## End(Not run)

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