tableHWE {SNPassoc}

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://csg.sph.umich.edu/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)