gaston (version 1.4.9)

set.hwe: Hardy-Weinberg Equilibrium

Description

Returns an updated bed.matrix with a new variable for the $p$-values of an Hardy-Weinberg Equilibrium test.

Usage

set.hwe(x, method = c("chisquare", "exact"), verbose = getOption("gaston.verbose", TRUE))

Arguments

x

A bed.matrix

method

The method to use, either "chisquare" or "exact"

verbose

If TRUE, display information on the function actions

Value

A bed.matrix similar to x, with a new variable x@snps$hwe containing the $p$-values for each SNP.

Details

Two tests of Hardy-Weinberg Equilibrium are proposed:

• if method = "chisquare", the good old Chi-square test
• if method = "exact", Haldane's exact test (see Wigginton et al)

The function set.stats will be called first if necessary.

The $p$-value is set to $1.0$ for SNPs on chromosomes Y and MT. For SNPs on chromosomes X, currently, the test is performed using only the genotypic counts of women.

References

Wigginton, J. E., Cutler, D. J., & Abecasis, G. R. (2005). A note on exact tests of Hardy-Weinberg equilibrium. The American Journal of Human Genetics, 76(5), 887-893

See Also

set.stats, set.genomic.sex

Examples

# Load data
data(LCT)
x <- as.bed.matrix(LCT.gen, LCT.fam, LCT.bim)

# Compute Hardy-Weinberg p-values
x <- set.hwe(x)
head( x@snps[,c("id","hwe")] )