HWE.exact {GeneticsBase}R Documentation

Exact test for Hardy-Weinberg Equilibrium for a biallelic locus

Description

Exact test for Hardy-Weinberg Equilibrium for a biallelic locus.

Usage

HWE.exact(object, 
          marker, 
          founderOnly=TRUE)

Arguments

object a geneSet object.
marker marker name for the biallelic locus.
founderOnly Indicates if only founders are used to do the test.

Value

The function HWE returns a list with class htest containing the following elements:

statistic A 3-element vector records the genotype frequencies: N11, N12, N22.
parameter A 2-element vector records the allele frequencies: N1 and N2
p.value p-value of the test.
method Information indicates if chisquare method or exact method is used to do HWE test.
data.name name of the data set
observed a table lists allele levels, allele pairs, and allele codes

Note

This function only works for genotypes with exactly 2 alleles.

Author(s)

David Duffy davidD@qimr.edu.au with modifications by Gregory R. Warnes, and Nitin Jain

References

Emigh TH. (1980) "Comparison of tests for Hardy-Weinberg Equilibrium", Biometrics, 36, 627-642.

See Also

HWE.chisq

Examples

library(GeneticsBase)
data(CAMP)

HWE.exact(CAMP, marker="m654")


[Package GeneticsBase version 1.6.0 Index]