tableHWE {SNPassoc} | R Documentation |
Test the null hypothesis that Hardy-Weinberg equilibrium holds in cases, controls and both populations.
tableHWE(x, strata) print.tableHWE(x, digits=4, sig=0.05, na="-", ...)
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 |
This function calculates the HWE test for those variables of class 'snp' in the object x of class 'setupSNP'
A matrix with p values for Hardy-Weinberg Equilibrium
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
Wigginton JE, Cutler DJ and Abecasis GR (2005). A note on exact tests of Hardy-Weinberg equilibrium. Am J Hum Genet 76:887-93
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)