swapbc1: Sample BC1 or Recombinant Inbred loci via approximate...

In bqtl: Bayesian QTL Mapping Toolkit

Sample BC1 or Recombinant Inbred loci via approximate posterior.

Description

An MCMC sampler for loci using precomputed dispersion matrices, various priors, and a pre-selected set of variables. For use with BC1 (backcross) designs and recombinant inbred lines.

Usage

swapbc1(varcov, invars, rparm, nreps, ana.obj, locs=NULL,
locs.prior=NULL, tol=1e-10 )

Arguments

varcov	The result of make.varcov
rparm	Scalar or vector with nrow(varcov$var.x) elements; the 'ridge' parameters for the independent variables - larger values imply more shrinkage or a more concentrated prior for the regresion coefficients.
nreps	How many cycles of MCMC to perform
ana.obj	A object produced by make.analysis.obj
invars	Which variables to start in the model. The first of these is immediately removed, so it is merely a placeholder. The number of genes in the model is therefore k <- length(invars)
locs	The columns of varcov\$var.x to use. The default uses all of them.
locs.prior	The prior mass to associate with each variable. Typically, these sum to one, but sometimes they might each be set to one (as in computing lod scores).
tol	Used in forming QR decomposition. Let it be.

Details

An MCMC sampler for loci using the object of make.varcov is executed. This sampler uses the exact posterior probability under the assumed correctness of the regression model using expected genotypes given marker values. This amounts to linearizing the likelihood with respect to the (possibly unknown) locus states. For models where the loci are fully informative markers this is the true posterior.

The chain is implemented as follows: given a set of regressor variables to start, one variable is removed, all regressor variables not in the model are examined to determine the effect of each on the posterior. One variable is sampled. The process is repeated until each variable has been removed and a new one sampled in its place (possibly the same variable that was removed is sampled). And this whole cycle is repeated nreps times.

Value

A list with components:

config	A k by k by nreps array of the locations sampled in each iteration.
posteriors	A vector of length k*nreps with the posteriors of the models.
coefs	A k by k matrix of the regression coefficients.
call	The call to swapbc1
cond	The k*nreps posterior probabilities of the k-1 gene models.
marg	The k*nreps marginal posteriors for all k gene models that could be formed using the current k-1 gene model
alt.marginal	A vector with length(locs) elements. At each step, the posterior associated with each candidate locus is added to an element of this vector. After all steps are finished, the result is normalized to sum to one. This turns out to be an exceedingly stable estimate of the marginal posterior.
alt.coef	A vector with length(locs) elements. At each step, the product of each posterior times the coefficient associated with a candidate locus is added to an element of this vector. After all steps are finished, the result is normalized by the total marginal posterior. This turns out to be an exceedingly stable estimate of the marginal (over all models) posterior mean of the regression coefficients.

Author(s)

Charles C. Berry [e-mail]

References

Berry C.C. (1998) Computationally Efficient Bayesian QTL Mapping in Experimental Crosses. ASA Proceedings of the Biometrics Section, 164-169.

See Also

swapf2

bqtl documentation built on Sept. 25, 2024, 1:08 a.m.