The Bayesian QTL models via a likelihood that is linearized w.r.t. a fixed genetic model. By default, all one and two gene models (without epistasis) are fitted and a MCMC sampler is used to fit 3,4, and 5 gene and (optionally) larger models.
linear.bayes(x, ana.obj, partial=NULL, rparm, specs,
scope, subset, casewt, ...)
The object returned by twohk
A list of objects returned by calls to
swap. Element i in swaps is for i gene
models.
A list of objects returned by calls to
summary.swap. Some elements may be NULL if no
samples were requested or if the sampling process yielded degenerate
results. Usually, this happens if no posterior is specified for the
regression coefficients, i.e. if rparm=0 was used or implied
A Vector of odds (relative to a no gene setup) for each
model size evaluated. The odds are computed under a prior that
places equal weights on models of each size considered (and are,
therefore, Bayes Factors). If models of size 1 and 2 are not
evaluated or if some degenerate results were encountered, this will
be NULL
A vector of posterior means of the regression
coefficients. If models of size 1 and 2 are not
evaluated or if some degenerate results were encountered, this will
be NULL
A vector of locus-wise posterior probabilities
that the interval covered by this locus contains a gene.If models of
size 1 and 2 are not evaluated or if some degenerate results were
encountered, this will be NULL
The call that generated this object
a formula giving the QTL and the candidate loci or a
varcov object
An analysis.object, see make.analysis.obj
a formula giving covariates to be controlled
A ridge parameter. A value of 1 is suggested, but the default is 0.
An optional list with components gene.number (to
indicate the model sizes), burn.in (to indicate the number of
initial MCMC cycles to discard), and n.cycles (to indicate how
many MCMC cycles to perform for each model size). If no values are
supplied, specs defaults to
list(gene.number=c(1,2,3,4,5),burn.in=1,n.cycles=c(0,0,200,100,100))
Not generally used. If supplied this will be passed to
varcov.
Not generally used. If supplied this will be passed to
varcov.
Not generally used. If supplied this will be passed to
varcov.
optional arguments to pass to twohk and swap
Charles C. Berry cberry@ucsd.edu
This function is a wrapper for
varcov, twohk, swap, and
summary.swap, and a better understanding of optional
arguments and the object generated is gained from their
documentation.
Berry C.C.(1998) Computationally Efficient Bayesian QTL Mapping in Experimental Crosses. ASA Proceedings of the Biometrics Section. 164--169.
data( little.ana.bc )
little.lin <- linear.bayes( bc.phenotype~locus(all), little.ana.bc, rparm=1 )
par(mfrow=c(2,3))
plot( little.ana.bc, little.lin$loc.posterior, type="h" )
little.lin$odds
par(mfrow=c(1,1))
plot(fitted(little.lin), residuals(little.lin))
rm(little.lin,little.ana.bc)
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