Chi square tests for Hardy Weinberg equilibrium
HWChisq performs the chi-square test for Hardy-Weinberg
equilibrium both for autosomal and X-chromosomal markers.
HWChisq(X, cc = 0.5, verbose = TRUE, x.linked = FALSE, phifixed = NULL)
X |
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cc |
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verbose |
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x.linked |
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phifixed |
(For X-chromosomal markers only)
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HWChisq does a chi-square test for Hardy-Weinberg equilibrium,
and by default applies a continuity correction. For extreme allele
frequencies, the continuity correction can lead to excessive type 1
error rates, and is better turned off in that case. The continuity
correction can be turned off by specifying cc=0.
HWChisq can do the chi-square test for both autosomal and
X-chrosomal markers. By setting x.linked = TRUE the marker
will be assumed to be on the X-chromosome, and the count vector
supplied should have 5 elements instead of 3 elements for an
autosomal marker. For X-chromsomal markers argument phifixed
is in general best left to its default value (NULL). Only in
specific situations where the theoretical population sex ratio is known (e.g. in
simulation studies where a universe with known gender ratio is
sampled) phifixed could be set to the theoretical ratio of interest.
When alternative is set to less, a one-sided test for
against a negative inbreeding coefficient (heterozygote excess) is
performed. When alternative is set to greater a one-sided test for
against a positive inbreeding coefficient (lack of heterozygotes) is
performed.
HWChisq returns a list with the components:
chisq |
value of the chi-square statistic. NA is returned if the marker is monomorphic. |
pval |
p-value of the chi-square test for Hardy-Weinberg equilibrium. |
D |
Half the deviation from Hardy-Weinberg equilibrium for the AB genotype. |
p |
the allele frequency of A. |
f |
the inbreeding coefficient. |
expected |
the expected counts under Hardy-Weinberg equilibrium |
Jan Graffelman jan.graffelman@upc.edu
Weir, B.S. (1996) Genetic data analysis II. Sinauer Associates, Massachusetts. See Chapter3.
For the chi-square test for X-linked markers:
Graffelman, J. & Weir, B.S. (2016) Testing for Hardy-Weinberg equilibrium at bi-allelic genetic markers on the X chromosome. Heredity 116(6) pp. 558–568. doi: 10.1038/hdy.2016.20
# # Test for an autosomal blood group marker # x <- c(MM=298,MN=489,NN=213) HW.test <- HWChisq(x,verbose=TRUE) # # Same test without continuity correction # HW.test <- HWChisq(x,cc=0,verbose=TRUE) # # Test for an X-chromsomal SNP. # rs5968922 <- c(A=392, B=212, AA=275, AB=296, BB=80) HW.test <- HWChisq(rs5968922,cc=0,x.linked=TRUE,verbose=TRUE)
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