HWExactPrevious: Exact test for Hardy-Weinberg equilibrium

In HardyWeinberg: Statistical Tests and Graphics for Hardy-Weinberg Equilibrium

Exact test for Hardy-Weinberg equilibrium

Description

HWExactPrevious performs an exact test for Hardy-Weinberg equilibrium

Usage

HWExactPrevious(X, alternative = "two.sided", pvaluetype = "selome",
x.linked = FALSE, verbose = FALSE)

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.
verbose	print results or not.

Details

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

For large samples, HWExactPrevious 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.

See Also

HWLratio, HWChisq

Examples

#
# Example autosomal marker
#
x <- c(298,489,213)
names(x) <- c("MM","MN","NN")
## Not run: HW.test <- HWExactPrevious(x,verbose=TRUE)
#
# Example x-linked marker
#
rs5968922  <- c(A=392, B=212, AA=275, AB=296, BB=80 )
## Not run: HWExactPrevious(rs5968922,x.linked=TRUE,verbose=TRUE) 

HardyWeinberg documentation built on May 7, 2022, 5:05 p.m.