lik.multin: Utility Function
In sergioventurini/HWEintrinsic: Objective Bayesian Testing for the Hardy-Weinberg Equilibrium Problem

lik.multin

R Documentation

Utility Function

Description

This function provides the value of the likelihood function of the full (unrestricted) model, as described in Consonni et al. (2011).

Usage

lik.multin(y, p11, p21)

Arguments

`y`	an object of class "HWEdata".
`p11`	gentotype proportion for the alleles pair `A_{1}A_{1}`.
`p21`	gentotype proportion for the alleles pair `A_{2}A_{1}`.

Details

This function has been used to generate the likelihood contours that appear in Figure 4 of Consonni et al. (2011) (see the example below).

Value

This function returns the numerical value of the likelihood in correspondence of the argument values.

Note

This function provides the likelihood function value only for the two alleles case.

Author(s)

Sergio Venturini sergio.venturini@unicatt.it

References

Consonni, G., Moreno, E., and Venturini, S. (2011). "Testing Hardy-Weinberg equilibrium: an objective Bayesian analysis". Statistics in Medicine, 30, 62–74. https://onlinelibrary.wiley.com/doi/10.1002/sim.4084/abstract

Examples

# The following code reproduces Figure 4 in Consonni et al. (2011) #
## Not run: 
# ATTENTION: it may take a long time to run! #

data(simdata)
n <- sum(dataset1@data.vec, na.rm = TRUE)
f <- c(.1,.5,1)
t <- round(f*n)
p11 <- p21 <- seq(0,1,length.out=100)
ip <- array(NA,c(length(f),length(p11),length(p21)))
for (k in 1:length(f)) {
	ip[k,,] <- outer(X = p11, Y = p21, FUN = Vectorize(ip.tmp), t[k])
	print(paste(k," / ",length(f),sep=""), quote = FALSE)
}

r <- 2
R <- r*(r + 1)/2
l <- 4
tables <- matrix(NA, nrow = R, ncol = l)
tables[, 1] <- dataset1@data.vec
tables[, 2] <- dataset2@data.vec
tables[, 3] <- dataset3@data.vec
tables[, 4] <- dataset4@data.vec
lik <- array(NA, c(l, length(p11), length(p21)))
M <- 300000
par(mfrow = c(4, 4))
for (k in 1:l) {
	y <- new("HWEdata", data = tables[, k])
	lik[k,,] <- lik.multin(y, p11, p21)
	
	nlev <- 10
	for (q in 1:length(f)) {
		contour(p11, p21, ip[q,,], xlab = expression(p[11]),
				ylab = expression(p[21]), nlevels = nlev, col = gray(0),
				main = "", cex.axis = 1.75, cex.lab = 1.75, labcex = 1.4)
		lines(p11^2, 2*p11*(1 - p11), lty = "longdash", col = gray(0), lwd = 2)
		contour(p11, p21, lik[k,,], nlevels = nlev, add = TRUE,
				col = gray(.7), labcex = 1.2)
		abline(a = 1, b = -1, lty = 3, col = gray(.8))
	}
	hwe.ibf.plot(y = y, t.vec = seq(1,n,1), M = M)
}

## End(Not run)

sergioventurini/HWEintrinsic documentation built on Oct. 19, 2023, 12:40 a.m.