set.hwe: Hardy-Weinberg Equilibrium

In gaston: Genetic Data Handling (QC, GRM, LD, PCA) & Linear Mixed Models

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

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.

Value

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

Author(s)

Hervé Perdry and Claire Dandine-Roulland

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")] )

gaston documentation built on Dec. 28, 2022, 1:30 a.m.