HWExactPrevious  R Documentation 
HWExactPrevious
performs an exact test for HardyWeinberg equilibrium
HWExactPrevious(X, alternative = "two.sided", pvaluetype = "selome", x.linked = FALSE, verbose = FALSE)
X 
vector with the genotype counts AA, AB, BB 
alternative 

pvaluetype 
if 
x.linked 

verbose 
print results or not. 
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
maxppsize 100000
or higer values. However, with such large
samples the exact test will give virtually the same result as a
chisquare test, and it may be easier to use HWChisq
in these
circumstances.
pval 
pvalue 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 
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 HardyWeinberg equilibrium, American Journal of Human Genetics (76) pp. 887893.
HWLratio
, HWChisq
# # Example autosomal marker # x < c(298,489,213) names(x) < c("MM","MN","NN") ## Not run: HW.test < HWExactPrevious(x,verbose=TRUE) # # Example xlinked marker # rs5968922 < c(A=392, B=212, AA=275, AB=296, BB=80 ) ## Not run: HWExactPrevious(rs5968922,x.linked=TRUE,verbose=TRUE)
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