Estimate Disequilibrium and Test for Hardy-Weinberg Equilibrium
Estimate disequilibrium parameter and test the null hypothesis that Hardy-Weinberg equilibrium holds.
HWE.test(x, ...)
## S3 method for class 'genotype'
HWE.test(x, exact = nallele(x)==2, simulate.p.value=!exact,
B=10000, conf=0.95, ci.B=1000, ... )
## S3 method for class 'data.frame'
HWE.test(x, ..., do.Allele.Freq=TRUE, do.HWE.test=TRUE)
## S3 method for class 'HWE.test'
print(x, show=c("D","D'","r","table"), ...)x |
genotype or haplotype object. |
exact |
a logical value indicated whether the p-value should be computed using the exact method, which is only available for 2 allele genotypes. |
simulate.p.value |
a logical value indicating whether the p-value
should be computed using simulation instead of using the
Chi-Square approximation. Defaults to |
B |
Number of simulation iterations to use when
|
conf |
Confidence level to use when computing the confidence level for D-hat. Defaults to 0.95, should be in (0,1). |
ci.B |
Number of bootstrap iterations to use when computing the confidence interval. Defaults to 1000. |
show |
a character vector containing the names of HWE test statistics to display from the set of "D", "D'", "r", and "table". |
... |
optional parameters passed to |
do.Allele.Freq |
logicial indication whether to summarize allele frequencies. |
do.HWE.test |
logicial indication whether to perform HWE tests |
HWE.test calls diseq to computes the Hardy-Weinberg
(dis)equilibrium statistics D, D', and r (correlation coefficient).
Next it calls diseq.ci to compute a bootstrap confidence
interval for these estimates. Finally, it calls
chisq.test to compute a p-value for Hardy-Weinberg
Equilibrium using a simulation/permutation method.
Using bootstrapping for the confidence interval and simulation for the p-value avoids reliance on the assumptions the underlying Chi-square approximation. This is particularly important when some allele pairs have small counts.
For details on the definition of D, D', and r, see the help page for
diseq.
An object of class HWE.test with components
diseq |
A |
ci |
A |
test |
A |
call |
function call used to creat this object. |
conf, B, ci.B, simulate.p.value |
values used for these arguments. |
Gregory R. Warnes greg@warnes.net
## Marker with two alleles:
example.data <- c("D/D","D/I","D/D","I/I","D/D",
"D/D","D/D","D/D","I/I","")
g1 <- genotype(example.data)
g1
HWE.test(g1)
## Compare with individual calculations:
diseq(g1)
diseq.ci(g1)
HWE.chisq(g1)
HWE.exact(g1)
## Marker with three alleles: A, C, and T
three.data <- c(rep("A/A",16),
rep("C/A",40),
rep("C/T",40),
rep("C/C",20),
rep("T/T",6))
g3 <- genotype(three.data)
g3
HWE.test(g3, ci.B=10000)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.