BGmix: Fit the BGmix differential expression model.

Description Usage Arguments Details Value Author(s) References Examples

Description

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

Usage

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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).

Author(s)

Alex Lewin

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

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## 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)

BGmix documentation built on Nov. 1, 2018, 4:30 a.m.