HardyWeinberg (version 1.6.1)

HWPerm.mult: Permutation tests fo variants with multiple alleles

Description

Function HWPerm.mult implements permutation tests for Hardy-Weinberg equilibrium for autosomal and X-chromosomal variants.

Usage

HWPerm.mult(x, y = NULL, nperm = 17000, eps = 0, verbose = TRUE, ...)

Arguments

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 that can be set for comparing probabilities in order to include tied outcomes

verbose

print output or not

…

addtional arguments

Value

pofthesample

probability of the observed sample

pseudodist

probabilities of simulated samples

pval

p-value

Details

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.

References

Graffelman, J. and Weir, B.S. (2017) Multi-allelic exact tests for Hardy-Weinberg equilibrium that account for gender. doi: 10.1101/172874 bioRxiv preprint

See Also

HWPerm

Examples

# NOT RUN {
#
# bi-allelic autosomal
#

x1 <- c(AA=298,AB=489,BB=213)
# }
# NOT RUN {
out <- HWPerm.mult(x1)
# }
# 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)
# }
# 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)
# }
# 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)
# }
# 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)
# }
# NOT RUN {
# }