hwe.jags: Hardy-Weinberg equlibrium test for a multiallelic marker...

In gap: Genetic Analysis Package

Hardy-Weinberg equlibrium test for a multiallelic marker using JAGS

Description

Hardy-Weinberg equlibrium test for a multiallelic marker using JAGS

Usage

hwe.jags(
  k,
  n,
  delta = rep(1/k, k),
  lambda = 0,
  lambdamu = -1,
  lambdasd = 1,
  parms = c("p", "f", "q", "theta", "lambda"),
  ...
)

Arguments

k	number of alleles.
n	a vector of k(k+1)/2 genotype counts.
delta	initial parameter values.
lambda	initial parameter values.
lambdamu	initial parameter values.
lambdasd	initial parameter values.
parms	monitored parmeters.
...	parameters passed to jags, e.g., n.chains, n.burnin, n.iter.

Details

Hardy-Weinberg equilibrium test.

This function performs Bayesian Hardy-Weinberg equilibrium test, which mirrors hwe.hardy, another implementation for highly polymorphic markers when asymptotic results do not hold.

Value

The returned value is a fitted model from jags().

Author(s)

Jing Hua Zhao, Jon Wakefield

References

\insertRef

wakefield10gap

See Also

hwe.hardy

Examples

## Not run: 
ex1 <- hwe.jags(4,c(5,6,1,7,11,2,8,19,26,15))
print(ex1)
ex2 <- hwe.jags(2,c(49,45,6))
print(ex2)
ex3 <- hwe.jags(4,c(0,3,1,5,18,1,3,7,5,2),lambda=0.5,lambdamu=-2.95,lambdasd=1.07)
print(ex3)
ex4 <- hwe.jags(9,c(1236,120,3,18,0,0,982,55,7,249,32,1,0,12,0,2582,132,20,1162,29,
                    1312,6,0,0,4,0,4,0,2,0,0,0,0,0,0,0,115,5,2,53,1,149,0,0,4),
                delta=c(1,1,1,1,1,1,1,1,1),lambdamu=-4.65,lambdasd=0.21)
print(ex4)
ex5 <- hwe.jags(8,n=c(
         3,
         4, 2,
         2, 2, 2,
         3, 3, 2, 1,
         0, 1, 0, 0, 0,
         0, 0, 0, 0, 0, 1,
         0, 0, 1, 0, 0, 0, 0,
         0, 0, 0, 2, 1, 0, 0, 0))
print(ex5)

# Data and code accordining to the following URL,
# http://darwin.eeb.uconn.edu/eeb348-notes/testing-hardy-weinberg.pdf
hwe.jags.ABO <- function(n,...)
{
  hwe <- function() {
     # likelihood
     pi[1] <- p.a*p.a + 2*p.a*p.o
     pi[2] <- 2*p.a*p.b
     pi[3] <- p.b*p.b + 2*p.b*p.o
     pi[4] <- p.o*p.o
     n[1:4] ~ dmulti(pi[],N)
     # priors
     a1 ~ dexp(1)
     b1 ~ dexp(1)
     o1 ~ dexp(1)
     p.a <- a1/(a1 + b1 + o1)
     p.b <- b1/(a1 + b1 + o1)
     p.o <- o1/(a1 + b1 + o1)
  }
  hwd <- function() {
     # likelihood
     pi[1] <- p.a*p.a + f*p.a*(1-p.a) + 2*p.a*p.o*(1-f)
     pi[2] <- 2*p.a*p.b*(1-f)
     pi[3] <- p.b*p.b + f*p.b*(1-p.b) + 2*p.b*p.o*(1-f)
     pi[4] <- p.o*p.o + f*p.o*(1-p.o)
     n[1:4] ~ dmulti(pi[],N)
     # priors
     a1 ~ dexp(1)
     b1 ~ dexp(1)
     o1 ~ dexp(1)
     p.a <- a1/(a1 + b1 + o1)
     p.b <- b1/(a1 + b1 + o1)
     p.o <- o1/(a1 + b1 + o1)
     f ~ dunif(0,1)
  }
  N <- sum(n)
  ABO.hwe <- R2jags::jags(list(n=n,N=N),,c("pi","p.a","p.b","p.o"),hwe,...)
  ABO.hwd <- R2jags::jags(list(n=n,N=N),,c("pi","p.a","p.b","p.o","f"),hwd,...)
  invisible(list(hwe=ABO.hwe,hwd=ABO.hwd))
}
hwe.jags.ABO.results <- hwe.jags.ABO(n=c(862, 131, 365, 702))
hwe.jags.ABO.results

## End(Not run)

gap documentation built on Sept. 11, 2024, 5:36 p.m.