HWTriExact {HardyWeinberg}

Exact test for Hardy-Weinberg equilibrium and equality of allele frequencies for tri-allelic variants.

Description

Function HWTriExact does a standard exact test for Hardy-Weinberg equilibrium of a tri-allelic variant, and also does joint exact tests for equilibrium and equality of allele frequencies if the genotype counts are given separately for both sexes

Usage

HWTriExact(x, y = NULL, eps = 1e-10, nperm = 17000, verbose = TRUE)

Arguments

x

vector with 6 genotype counts (AA,AB,AC,BB,BC,CC)

y

vector with 6 or 3 genotype counts (AA,AB,AC,BB,BC,CC) or (A,B,C)

eps

a tolerance that can be set for comparing exact probabilities

nperm

number of permutations (only relevant for autosomal stratified by gender)

verbose

print output or not

Details

If only x is specified, an exact test for an autosomal variant with three alleles will be performed.

If both x and y are supplied as vectors with 6 elements, a permutation test for HWE and equality of allele frequencies (EAF) for an autosomal variant is performed, using nperm permutations. The distribution of the probabilities is returned in pseudodist. The computational cost of a completed enumeration algorithm can be prohibitive in this case.

If x is supplied as a length 6 vector, and y as a length 3 vector, the variant is assumed to be X-chromosomal, x containing female genotype counts and y containing male genotyep counts. In this case a joint exact test for HWE and EAF for an X-chromosomal tri-allelic variant is executed.

See the examples in the example section below.

Value

pval

The p-value of the sample

pseudodist

Distribution of probabilities obtained by simulation

pofthesample

The probability of the observed sample

Author(s)

Jan Graffelman [e-mail]

References

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.

See Also

HWPerm.mult

Examples

#
# Autosomal tri-allelic (not accounting for gender)
#

x <- c(AA=20,AB=31,AC=26,BB=15,BC=12,CC=0)
## Not run: out <- HWTriExact(x)

#
# Autosomal tri-allelic accounting for gender
#

males   <- c(A=1,B=21,C=34) 
females <- c(AA=0,AB=1,AC=0,BB=8,BC=24,CC=15)
## Not run: out <- HWTriExact(females,males)

#
# X-chromosomal tri-allelic accounting for gender
#

males   <- c(A=1,B=21,C=34) 
females <- c(AA=0,AB=1,AC=0,BB=8,BC=24,CC=15)
## Not run: out <- HWTriExact(females,males)