BGmix-package: BGmix fits a variety of Bayesian hierarchical models for...

Description Details Author(s) References Examples

Description

BGmix uses a C++ routine to fit the chosen model via an MCMC algorithm. Files are written to a sub-directory in the working directory. The package includes R functions for reading the results into R, and several plotting functions and functions for estimating error rates.

Details

Package: BGmix
Type: Package
Version: 1.0
Date: 2007-02-01
License: GPL

See Vignette for details of how to use this package (use openVignette()).

Author(s)

Alex Lewin and Natalia Bochkina

Maintainer: Alex Lewin <[email protected]>

References

Lewin, A., Bochkina, N. and Richardson, S. (2007), Fully Bayesian mixture model for differential gene expression: simulations and model checks. http://www.bgx.org.uk/publications.html

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
## Note this is a very short MCMC run!
## For good analysis need proper burn-in period.
data(ybar,ss)
outdir <- BGmix(ybar, ss, c(8,8), nburn=0, niter=100, nthin=1,trace.pred=1)

## Basic plot of parameters
params <- ccParams(outdir)
plotBasic(params,ybar,ss)

## plots of FDR and related quantities
fdr <- calcFDR(params)
par(mfrow=c(1,2))
plotFDR(fdr)

## plots of Bayesian p-values
## for predictive checks of mixture prior 
pred <- ccPred(outdir,q.trace=TRUE)
plotPredChecks(pred$pval.ybar.mix2,params$pc,probz=0.5)

## plots of predictive density superimposed on data
plotMixDensity(params,pred,ybar,ss)

BGmix documentation built on May 6, 2019, 2:29 a.m.