set.hwe | R Documentation |
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 |
A |
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
set.stats
, set.genomic.sex
# 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")] )
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