Permutation tests fo variants with multiple alleles
Function HWPerm.mult implements permutation tests for
Hardy-Weinberg equilibrium for autosomal and X-chromosomal variants.
HWPerm.mult(x, y = NULL, nperm = 17000, eps = 1e-10, verbose = TRUE, ...)
x |
vector or triangular matrix with male genotype counts |
y |
vector or triangular matrix with female genotype counts |
nperm |
number of permutations (17.000 by default) |
eps |
a tolerance for the comparison of floating point numbers |
verbose |
print output or not |
... |
addtional arguments |
This function approximates exact test probabilities for joint tests
for HWE and equality of allele frequencies for variants with multiple
alleles. For purely bi-allelic variant HWPerm can be used which
allows for more statistics than just probabilities.
If argument y is not specified, gender is considered
irrelevant, and x contains total genotype counts. If x
and y are specified, x should contain male genotype
counts and y female genotype counts. x and y can
be vectors if the variant is bi-allelic, but are assumed lower
triangular if there are more than two alleles. x is still a
vector if there are multiple alleles but the variant is
X-chromosomal. See the examples given below.
pofthesample |
probability of the observed sample |
pseudodist |
probabilities of simulated samples |
pval |
p-value |
Jan Graffelman jan.graffelman@upc.edu
Graffelman, J. and Weir, B.S. (2017) Multi-allelic exact tests for Hardy-Weinberg equilibrium that account for gender. Molecular Ecology Resources. 18(3) pp. 461–473. doi: 10.1111/1755-0998.12748
# # bi-allelic autosomal # x1 <- c(AA=298,AB=489,BB=213) ## Not run: out <- HWPerm.mult(x1) ## End(Not run) # # bi-allelic X-chromosomal # x2.m <- c(A=39, B=21) x2.f <- toTriangular(c(AA=28, AB=30, BB=8)) ## Not run: out <- HWPerm.mult(x2.m,x2.f) ## End(Not run) # # autosomal k alleles not accounting for gender # x3 <- c(AA=12,AB=19,AC=13,BB=7,BC=5,CC=0) x3 <- toTriangular(x3) ## Not run: out <- HWPerm.mult(x3) ## End(Not run) # # X-chromosomal k alleles # x4.m <- c(A=15,B=17,C=24) x4.f <- toTriangular(c(AA=4,AB=2,AC=13,BB=6,BC=19,CC=4)) ## Not run: out <- HWPerm.mult(x4.m,x4.f) ## End(Not run) # # Autosomal k alleles accounting for gender # x5.m <- toTriangular(c(AA=12,AB=19,AC=13,BB=7,BC=5,CC=0)) x5.f <- toTriangular(c(AA=8,AB=12,AC=13,BB=8,BC=7,CC=0)) ## Not run: out <- HWPerm.mult(x5.m,x5.f) ## End(Not run) # # Autosomal STR with multipe alleles # data(NistSTRs) A1 <- NistSTRs[,1] A2 <- NistSTRs[,2] GenotypeCounts <- AllelesToTriangular(A1,A2) print(GenotypeCounts) ## Not run: out <- HWPerm.mult(GenotypeCounts) ## End(Not run)
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