Nothing
set.hwe <- function(x, method = c("chisquare", "exact"), verbose = getOption("gaston.verbose",TRUE)) {
if( !all(c("N0", "N1", "N2") %in% names(x@snps) )) {
if(verbose) cat("Computing basic stats\n")
x <- set.stats(x)
}
w.a <- is.autosome(x@snps$chr)
w.x <- is.chr.x(x@snps$chr)
hwe <- rep(1.0, ncol(x) )
method <- match.arg(method)
if(method == 'chisquare') {
if(verbose) cat("Computing HW chi-square p-values\n")
hwe[w.a] <- .Call('gg_hwe_chi', PACKAGE = "gaston", x@snps$N0[w.a], x@snps$N1[w.a], x@snps$N2[w.a])
hwe[w.x] <- .Call('gg_hwe_chi', PACKAGE = "gaston", x@snps$N0.f[w.x], x@snps$N1.f[w.x], x@snps$N2.f[w.x])
} else {
if(verbose) cat("Computing HW exact test p-values\n")
hwe[w.a] <- .Call('gg_hwe', PACKAGE = "gaston", x@snps$N0[w.a], x@snps$N1[w.a], x@snps$N2[w.a])
hwe[w.x] <- .Call('gg_hwe', PACKAGE = "gaston", x@snps$N0.f[w.x], x@snps$N1.f[w.x], x@snps$N2.f[w.x])
}
x@snps$hwe <- hwe
x
}
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