BGmix: Fit the BGmix differential expression model.
In BGmix: Bayesian models for differential gene expression

Description Usage Arguments Details Value Author(s) References Examples

This is the main function of the BGmix package. It calls the C++ code which performs the MCMC to fit the BGmix model.

BGmix(ybar, ss, nreps, neffects = 2, xx = matrix(c(1, 1, -0.5, 0.5),
ncol = 2, byrow = T), ntau = NULL, indtau = NULL, jstar = 1, niter =
10000, nburn = 10000, nthin = 10, seed = 12345, move.choice.bz = 4,
move.choice.aa = 1, move.choice.lam = 0, move.choice.tau = 1,
move.choice.eta = 1, trace.out = 1, trace.pred = 0, sig.aa = 0.1,
tau.eps = 50, lambda.up.init=1.5, lambda.down.init=1.5,
datafilename.ybar = NULL, xfilename = NULL, itfilename =
NULL, rundir=".")

`ybar`	matrix no. genes x no. experimental conditions. Mean log gene expression for each gene in each condition.
`ss`	matrix no. genes x no. experimental conditions. Sample variance of log gene expression for each gene in each condition.
`nreps`	vector containing the number of replicate arrays in each experimental condition
`neffects`	number of effect parameters per gene (eg. 2 for unpaired differential expression)
`xx`	design matrix: no. effects x no. experimental conditions. See Vignette for specification of design matrix. Default is for unpaired differential expression.
`ntau`	number of variances per gene
`indtau`	label for each condition indicating which variance grouping that condition belongs to. See Vignette for more detail.
`jstar`	Label of the effect parameter which has the mixture prior. Labels start at 0, as in C++. If no parameter has a mixture prior, set jstar=-1.
`niter`	no. MCMC iterations after burn-in. This must be at least 100 for the function to work (or else set to zero).
`nburn`	no. MCMC iterations for burn-in. This must be at least 100 for the function to work (or else set to zero).
`nthin`	thinning parameter for MCMC iterations
`seed`	initial value for random seed
`move.choice.bz`	indicates choice of mixture prior: 1 for point mass null + Uniform alternatives, 4 for point mass null + Gamma alternatives, 5 for small Normal null + Gamma alternatives
`move.choice.aa`	if this is 1, hyperparameter a for gene variances is updated, if this is 0 it is fixed.
`move.choice.lam`	if this is 1, hyperparameter lambda for mixture prior is updated, if this is 0 it is fixed.
`move.choice.tau`	indicates choice of prior on gene variances: 1 for Inverse Gamma, 2 for log Normal.
`move.choice.eta`	if this is 1, hyperparameter eta for mixture prior is updated, if this is 0 it is fixed.
`trace.out`	if this is 1, output trace of model parameters, if this is 0, no output.
`trace.pred`	if this is 1, output trace of predictive quantities, if this is 0, no output.
`sig.aa`	step-size in random walk update for a (hyperparameter for gene variances distribution)
`tau.eps`	Value of epsilon used in the small Normal null mixture component.
`lambda.up.init`	init or fixed value of lambda+ (parameter of Gamma mixture component)
`lambda.down.init`	init or fixed value of lambda- (parameter of Gamma mixture component)
`datafilename.ybar`	character. Name describing the data set (by default this is taken from the name of the ybar argument).
`xfilename`	character. Name describing the design matrix.
`itfilename`	character. Name describing the indtau parameter.
`rundir`	character. Path for saving output files. A new sub-directory is created in the `rundir` directory.

The C++ code writes a count down on the screen, to give an indication of how long the code has to run. Output is written to a sub-directory of the working directory. This sub-directory is created automatically, and its name is printed by the C++ code to the screen.

The output directory is returned (character).

Alex Lewin

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)
BGmix(ybar, ss, c(8,8), nburn=0, niter=1000, nthin=1)