Merged SNP HWE

hwe.r

maf <- function(x) { sum(x) / (length(x) * 2)}

hwe <- function(x) {
	observed <- table(x)
	m <- maf(x)
	expected <- c(
		(1-m)^2, 2 * m * (1-m), m^2
	) * length(x) 
	chisq.test(rbind(observed, round(expected)))
	print(rbind(observed, round(expected)))
}


deletion <- rbinom(100000, 2, 0.123)
variant <- rbinom(100000, 2, 0.039)
probe <- 
abscaled <- round(ab / 2)
abscaled <- round(ab)

ab <- a
ab[b == 2] <- 0
ab[b == 1] <- a[b == 1] * 0.5
ab <- round(ab)

maf(a)
maf(b)
maf(ab)

hwe(a)
hwe(b)
hwe(ab)