BGmix

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Fit the BGmix differential expression model.

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

Keywords
models
Usage
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=".")
Arguments
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.
Details

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.

Value

The output directory is returned (character).

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

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