HardyWeinberg (version 1.7.8)

HWNetwork: 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)

Value

the exact p-value of the test.

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)

Author

Jan Graffelman

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.

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. tools:::Rd_expr_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)