GRENITS (version 1.24.0)

ReplicatesNet_gauss: Dynamic Bayesian Network Inference Using Linear Interactions and Gaussian Experimental Noise

Description

Run Bayesian inference of linear interaction network on data with replicates. The replicates are assumed to follow a Gaussian distribution. The function generates MCMC chains that can later be analysed.

Usage

ReplicatesNet_gauss(     resultsFolder,   timeSeries,           numReps,  ParamVec = NULL,   chains = 2, user.seeds = NULL,
		     Regulators = NULL, fixMe = NULL)

Arguments

resultsFolder

Name of output folder. The folder will be created and the output of the run will be placed there.

timeSeries

Data matrix containing gene expression time series. Where genes will be placed in rows and time points in columns. Each times series must be placed one after another, so that the first n columns correspond to time series replicate one, the next n columns to time series replicate two, etc. Gene names may be included as row names.

numReps

Number of replicate time series included in timeSeries matrix.

ParamVec

A parameter vector created using "mcmc.defaultParams_gauss". If none is given, default parameters will be used. The vector contains parameters associated to the priors as well as MCMC run length. (See mcmc.defaultParams_gauss)

chains

Number of MCMC chains to run.

user.seeds

An optional vector with seeds to use for MCMC chains.

Regulators

An optional vector with the indices of which genes are regulators. If provided, all non-regulator genes will not be allowed to regulate.

fixMe

An optional matrix of size genes x genes, where columns represent regulators and rows regulated genes. The matrix informs the model of network connections known to be present/absent. For each position use either 0 (no regulation, fix off), 1 (known regulatory interaction, fix on) or NaN (no information, do not fix).

Value

For each chain run, a folder (chain1, chain2, ...) will be created and the output of the MCMC run will be placed there. The files will be B_mcmc (the coeffcients of the linear regression), Gamma_mcmc (the indicator variables of Gibbs variable selection), Lambda_mcmc (the precision of each regression), Mu_mcmc (the intercept of each regression), Rho_mcmc (the network connectivity parameter), DataMean_standarised (a times series with the mean of the replicates), Lambda_exp_mcmc (the precision of the replicate noise) and Y_mean (the mean posterior value of the inferred "true mRNA").

Details

The order in which the replicates are placed do not affect the output. In other words swapping timepoint 2 replicate 1 and timepoint 2 replicate 2 makes no difference. For the cases where a measurement is not available, an NaN may be used.

References

Morrissey, E.R., Juarez, M.A., Denby, K.J. and Burroughs, N.J. 2010. On reverse engineering of gene interaction networks using time course data with repeated measurements. Bioinformatics 2010; doi: 10.1093/bioinformatics/btq421

See Also

mcmc.defaultParams_gauss, analyse.output.

Examples

  # Synthetic data
  data(Athaliana_ODE_4NoiseReps)
  # Folder where raw runs will be kept and later analysed
  output.folder <- paste(tempdir(), "/Example_ReplicatesNet_Gauss",sep="")
  # Run network inference and place raw results in output.folder
  ReplicatesNet_gauss(output.folder, Athaliana_ODE_4NoiseReps, numReps = 4)
  # Analyse raw results, place analysis plots and files in output.folder
  analyse.output(output.folder)