R: Test for Hardy-Weinberg Equilibrium

tableHWE {SNPassoc} | R Documentation

## Test for Hardy-Weinberg Equilibrium

### Description

Test the null hypothesis that Hardy-Weinberg equilibrium holds in cases, controls and both populations.

`print` print the information. Number of digits, and significance level can be changed

### Usage

    tableHWE(x, strata, ...)

### Arguments

`x` | an object of class 'setupSNP'
`strata` | a factor variable for a stratified analysis
`...` | optional arguments

### Details

This function calculates the HWE test for those variables of class 'snp' in the object x of class 'setupSNP'

### Value

A matrix with p values for Hardy-Weinberg Equilibrium

### Author(s)

This function is based on an R function which computes an exact SNP test of Hardy-Weinberg Equilibrium written by Wigginton JE, Cutler DJ and Abecasis GR available at http://www.sph.umich.edu/csg/abecasis/Exact/r_instruct.html

### References

Wigginton JE, Cutler DJ and Abecasis GR (2005). A note on exact tests of Hardy-Weinberg equilibrium. Am J Hum Genet 76:887-93

### See Also

`setupSNP`

### Examples

    data(SNPs)
    ans<-setupSNP(SNPs,6:40,sep="")
    res<-tableHWE(ans)
    print(res)
    #change the significance level showed in the flag column
    print(res,sig=0.001)

    #stratified analysis
    res<-tableHWE(ans,ans$sex)
    print(res)

[Package SNPassoc version 1.9-2 Index]