HWNetwork {HardyWeinberg}

Autosomal and X-chromosomal exact tests for HWE via a Network algorithm

Description

Program HWNetwork implements a network algorithm for efficient calculation of exact test p-values in HWE tests with multiple alleles.

Usage

HWNetwork(a1, a2, ma = NULL, fe = NULL, gender = NULL, verbose = TRUE)

Arguments

a1

the first allele (expressed as a number)

a2

the second allele (expressed as a number; NA if the variant is X chromosomal)

ma

alternative format: vector of male X chromosomal allele counts.

fe

triangular matrix of female genotype counts

gender

gender of the individual (1=male; 2=female)

verbose

be silent (verbose=FALSE) or informative (verbose=TRUE)

Details

Function HWNetwork accepts data in two formats. Original genotype data (e.g. repeat numbers of microsatellites) can be supplied, or the data can be supplied in summarized form as a male genotype count vector and a female genotype count matrix. If one of the two male alleles is missing (NA) the variant will taken to be X-chromosomal. If all males have two alleles, the variant will taken to be autosomal.

Value

the exact p-value of the test.

Author(s)

Jan Graffelman [e-mail]

References

Aoki, S. (2003) Network algorithm for the Exact Test of Hardy-Weinberg Proportion for Multiple Alleles. Biometrical Journal 45(4), pp. 471-490.

Engels, W. R. (2009) Exact Tests for Hardy-Weinberg Proportions. Genetics 183, pp. 1431-1441.

Graffelman, J. (2015) Exploring Diallelic Genetic Markers: The HardyWeinberg Package. Journal of Statistical Software 64(3): 1-23. doi:10.18637/jss.v064.i03.

See Also

HWExact, HWExactStats

Examples

#
# From vectors with counts of genotypes
#
data(TSIXTriAllelics)
ma <- as.matrix(TSIXTriAllelics[1,2:4])
names(ma) <- c("A","B","C")

fe <- TSIXTriAllelics[1,5:10]
names(fe) <- c("AA","AB","AC","BB","BC","CC")

fe <- HardyWeinberg:::toTriangularfixed(fe)

HWNetwork(ma=ma,fe=fe)