HWExact {HardyWeinberg}

Exact test for Hardy-Weinberg equilibrium

Description

HWExact performs an exact test for Hardy-Weinberg equilibrium

Usage

HWExact(X, alternative = "two.sided", pvaluetype = "selome", eps=1e-10, x.linked =
FALSE, verbose = TRUE)

Arguments

X

vector with the genotype counts AA, AB, BB

alternative

two.sided (default) will perform a two-sided test where both an excess and a dearth of heterozygotes count as evidence against HWE. less is a one-sided test where only dearth of heterozygotes counts a evidence against HWE, greater is a one-sided test where only excess of heterozygotes counts as evidence against HWE.

pvaluetype

if pvaluetype is set to dost then the p-value of a two-sided test is computed as twice the tail area of a one-sided test. When set to selome, the p-value is computed as the sum of the probabilities of all samples less or equally likely as the current sample. When set to midp, the p-value is computed as half the probability of the current sample + the probabilities of all samples that are more extreme.

x.linked

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

eps

a tolerance that can be set for comparing probabilities in order to include tied outcomes

verbose

print results or not.

Details

HWExact uses the recursion equations described by Wigginton et. al.

For testing large sets of bi-allelic variants, use the faster code in HWExactStats.

For large samples, HWExact may give the error message: "evaluation nested too deeply: infinite recursion". This can usually be resolved by increasing R's limit on nested expressions with options(expressions=10000) or a higher limit. With higher limits, the error message "protect(): protection stack overflow" can occur. This error can usually be resolved by increasing R's protection stack with the command line option --max-ppsize 100000 or higer values. However, with such large samples the exact test will give virtually the same result as a chi-square test, and it may be easier to use HWChisq in these circumstances.

Value

pval

p-value of the exact test

prob

probabilities of all possible samples with the same sample size and minor allele count

pofthesample

probability of the observed sample

Author(s)

Jan Graffelman ([e-mail])

References

Weir, B.S. (1996) Genetic data analysis II. Sinauer Associates, Massachusetts. See Chapter3.

Wigginton, J.E., Cutler, D.J. and Abecasis, G.R. (2005) A note on exact tests of Hardy-Weinberg equilibrium, American Journal of Human Genetics (76) pp. 887-893.

Graffelman, J. and Moreno, V. (2013) The mid p-value in exact tests for Hardy-Weinberg equilibrium, Statistical Applications in Genetics and Molecular Biology 12(4) pp. 433-448.

See Also

HWLratio, HWChisq, HWExactStats

Examples

#
# Example for an autosomal marker using the standard exact p-value
#
x <- c(298,489,213)
names(x) <- c("MM","MN","NN")
HW.test <- HWExact(x,verbose=TRUE)
#
# Example for an autosomal marker using the mid p-value
#
HW.test <- HWExact(x,verbose=TRUE,pvaluetype="midp")
#
# Example x-linked markers
#
rs5968922  <- c(A=392, B=212, AA=275, AB=296, BB=80 )
HWExact(rs5968922,x.linked=TRUE,verbose=TRUE)
#
#
#
y <- c(GG=48, CG=209, CC=277, G=129, C=337) 
HWExact(y,x.linked=TRUE)
#
#