Hardy-Weinberg Equilibrium
Returns an updated bed.matrix with a new variable for the p-values of an
Hardy-Weinberg Equilibrium test.
set.hwe(x, method = c("chisquare", "exact"),
verbose = getOption("gaston.verbose", TRUE))x |
|
method |
The method to use, either "chisquare" or "exact" |
verbose |
If |
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.
A bed.matrix similar to x, with a new variable x@snps$hwe
containing the p-values for each SNP.
Hervé Perdry and Claire Dandine-Roulland
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
# 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")] )Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.