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.

Usage

tableHWE(x, strata)
print.tableHWE(x, digits=4, sig=0.05, na="-", ...) 

Arguments

x an object of class 'setupSNP'
strata a factor variable for a stratified analysis
digits number of significant digits, see 'print.default'
sig significance level in the flag column
na character string (or 'NULL') indicating 'NA' values in printed output, see 'print.default
... further arguments passed to or from other methods

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 1.0-2 Index]