LambdaOptim {HWEBayes} | R Documentation |
In the single f model we may parameterize in terms of the allele frequencies and λ=log((f-f_{min})/(1-f)) where f_{min}=-p_{min}/(1-p_{min}) and p_{min} is the minimum allele frequency. The prior for λ is assumed normal and this function finds the mean and standard deviation of this normal, given two values for f, with associated probabilities.
LambdaOptim(nsim, bvec, f1, f2, p1, p2, init)
nsim |
the optimization is carried out by simulating from the joint prior on allele frequencies and λ, and this argument gives the number of simulations to take from the prior |
bvec |
vector of length k of prior specification for the HWE Dirichlet prior, where k is the number of alleles. |
f1 |
first quantile for inbreeding coefficient f |
f2 |
second quantile for inbreeding coefficient f |
p1 |
probability associated with f1
|
p2 |
probability associated with f2
|
init |
initial values for lambdamu and lambdasd
|
lambdamu |
prior mean for λ |
lambdasd |
prior standard deviation for λ |
This function can be unstable and good starting values may be needed. It is also recommended to check the output by simulating from the given prior to see if the empirical quantiles match with those desired; the function SinglefPrior
may be used for this
Jon Wakefield (jonno@u.washington.edu)
Wakefield, J. (2009). Bayesian methods for examining Hardy-Weinberg equilibrium. Biometrics.
HWEImportSamp
bvec <- c(1,1,1,1) init <- c(-3,log(1.1)) lampr <- LambdaOptim(nsim=10000,bvec=bvec,f1=0,f2=0.26,p1=0.5,p2=0.95,init)