BGmix-package

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BGmix fits a variety of Bayesian hierarchical models for finding differential gene expression between 2 or more experimental conditions.

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.

Keywords
models
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()).

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

Aliases
  • BGmix-package
Examples
## 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)
Documentation reproduced from package BGmix, version 1.32.0, License: GPL-2

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