bmapqtl.options {bim}R Documentation

Options Settings for BmapQTL

Description

This function allows the users to set and examine the options and priors for reversible jump MCMC QTL model search. The options are stored in global hidden variable .bmapqtl.options.

Usage

bmapqtl.options(...,reset=FALSE)

Arguments

reset reset options to default settings
... any options can be defined, using `name = value'. The available options are listed below.
prior.nqtl
one of "poisson", "geometric" or "uniform" (partial match OK). Default is "geometric".
mean.nqtl
prior for number of QTL (default = 3).
niter
number of iterations (default = 400000).
by
record every by iterations (default = 400).
burnin
proportion of iterations for burnin (default = .05).
preburn
proportion of burnin used for preburn (default = .05).
nqtl
initial number of QTL (default = 0).
init
2-vector with initial mean and variance (see details).
prior.mean
2-vector with prior for mean (see details).
prior.var
2-vector with prior for variance (see details).
prior.add
2-vector with prior for additive effects (see details).
prior.dom
2-vector with prior for dominance effects (see details).
seed
Random number seed. If 0(default), seed will be generated randomly.

Details

Initial mean and variance init are used directly if the variance is positive. For values c(a,-b) use mean 0 and variance .5s^2.

Prior arguments have coded meaning as follows, with a and b non-negative. For the grand mean, c(a,b) signifies Normal(a,b), while c(a,-b) stands for Normal(bar{Y},bS^2), with bar{Y} and S^2 the phenotype mean and variance, respectively. Additive and dominance priors coded as c(a,b) have Normal(a,b); as c(a,-b) have Normal(0,aS^2); as c(-a,-b) have Normal(0,β S^2) with βsimBeta(2,10) if a=b=0 or βsimBeta(a,b) otherwise. Variance has prior inverse Gamma: IG(a,b) for c(a,b), or IG(a,\eqn{s^2}) for c(a,-b).

Value

A list (in any case) with the previous values of the options changed, or all options when no arguments were given.

Author(s)

Hao Wu, hao@jax.org

See Also

options

Examples

bmapqtl.options()
bmapqtl.options(niter=100000, by=1000)

[Package bim version 1.01-1 Index]