HWExact {HardyWeinberg} | R Documentation |
HWExact
performs an exact test for Hardy-Weinberg equilibrium
HWExact(X, alternative = "two.sided", pvaluetype = "dost", verbose = FALSE)
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. |
verbose |
print results or not. |
HWExact
use the recursion equations described by Wigginton
et. al.
pval |
p-value of the exact test |
pofthesample |
probability of the observed sample |
HWExact
is designed for a fast analysis of a large set of
markers. HWExact
is slower, but provides more detailed
statistics for the sample under study.
Jan Graffelman (jan.graffelman@upc.edu)
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.
x <- c(298,489,213) names(x) <- c("MM","MN","NN") HW.test <- HWExact(x) print(HW.test)