BGmix-package {BGmix} | R Documentation |
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.
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()).
Alex Lewin and Natalia Bochkina
Maintainer: Alex Lewin <a.m.lewin@imperial.co.uk>
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
## 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)