HardyWeinberg (version 1.7.8)

HWPerm: Permutation test for Hardy-Weinberg equilibrium

Description

Function HWPerm does a permutation test for Hardy-Weinberg equilibrium using a user-supplied test statistic.

Usage

HWPerm(x, nperm = 17000, verbose = TRUE, x.linked = FALSE,
FUN = ifelse(x.linked,Chisquare.x,Chisquare), eps=1e-10, ...)

Value

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.

Arguments

x

A vector of genotype counts (AA,AB,BB)

nperm

The number of permutations

verbose

verbose = TRUE will print results, verbose = FALSE is silent.

x.linked

x.linked=FALSE indicates the marker is autosomal (default), and x.linked=TRUE indicates it resides on the X-chromosome.

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 FUN

Author

Jan Graffelman

Details

The set of alleles for the observed sample is permuted. Consequently, the test is conditional on allele frequency.

References

Ziegler, A. & Konig, I.R. (2006) A statistical approach to genetic epidemiology. Wiley.

See Also

HWChisq,HWExact,HWLratio

Examples

x <- c(MM=298,MN=489,NN=213)
if (FALSE) {
#
# use a default chi-square statistic
#
HW.test <- HWPerm(x,nperm=10000,verbose=TRUE)
#
# use a chi-square statistic with continuity correction.
#
HW.test <- HWPerm(x,nperm=10000,verbose=TRUE,
FUN=function(z) HWChisq(z,verbose=FALSE)$chisq,cc=0.5) # 
#
# use a likelihood ratio statistic.
#
HW.test <- HWPerm(x,nperm=10000,verbose=TRUE,
FUN=function(y) HWLratio(y,verbose=FALSE)$G2)
# 
# use an exact test p-value
#
HWPerm(x,nperm=10000,verbose=TRUE,FUN=function(y) 1-HWExact(y,verbose=FALSE)$pval)
# 
#
# 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)
}