Permutation test for Hardy-Weinberg equilibrium
Function HWPerm does a permutation test for Hardy-Weinberg
equilibrium using a user-supplied test statistic.
HWPerm(x, nperm = 17000, verbose = TRUE, x.linked = FALSE, FUN = ifelse(x.linked,Chisquare.x,Chisquare), eps=1e-10, ...)
x |
A vector of genotype counts (AA,AB,BB) |
nperm |
The number of permutations |
verbose |
|
x.linked |
|
FUN |
An function call for calculating the test statistic for HWE (see examples below) |
eps |
Tolerance for comparison of floating point numbers (1e-10 by default) |
... |
Additional parameters for the function call argument |
The set of alleles for the observed sample is permuted. Consequently, the test is conditional on allele frequency.
HWPerm returns a list with the components:
stat |
value of the chosen test statistic for the observed sample. |
pval |
p-value of the permutation test. |
Jan Graffelman jan.graffelman@upc.edu
Ziegler, A. & K\"onig, I.R. (2006) A statistical approach to genetic epidemiology. Wiley.
x <- c(MM=298,MN=489,NN=213) ## Not run: HW.test <- HWPerm(x,nperm=10000,verbose=TRUE) # uses default chi-square statistic HW.test <- HWPerm(x,nperm=10000,verbose=TRUE,function(z) HWChisq(z)$chisq,cc=0.5) # uses chi-square statistic with continuity correction. HW.test <- HWPerm(x,nperm=10000,verbose=TRUE,function(y) HWLratio(y)$G2) # uses likelihood ratio statistic. HWPerm(x,nperm=10000,verbose=TRUE,function(y) 1-HWExact(y)$pval) # uses exact test p-value # # Permutation test for a marker on the X chromosome # rs5968922 <- c(A=392, B=212, AA=275, AB=296, BB=80) HW.test <- HWPerm(rs5968922,nperm=10000,x.linked=TRUE,verbose=TRUE) ## End(Not run)
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