bmapqtl.options {bim}  R Documentation 
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.
bmapqtl.options(...,reset=FALSE)
reset 
reset options to default settings 
... 
any options can be defined, using `name = value'. The
available options are listed below.

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
nonnegative. 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)
.
A list (in any case) with the previous values of the options changed, or all options when no arguments were given.
Hao Wu, hao@jax.org
bmapqtl.options() bmapqtl.options(niter=100000, by=1000)