read.chain {GRENITS} | R Documentation

## Read MCMC Chains

### Description

Read MCMC chains for further analysis.

### Usage

    read.chain(output.folder, chainNumber)

### Arguments

`output.folder` | Name of folder (including path) where chains are kept
`chainNumber` | Which of the chains will be read

### Details

Read chains produced by NonLinearNet, LinearNet, ReplicatesNet_student and ReplicatesNet_gauss for further analysis.

### Value

Returns a list of vectors/matrices with the value of the variables at each MCMC iteration.

### 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

Morrissey, E.R., Juarez, M.A., Denby, K.J. and Burroughs, N.J. 2011 Inferring the time-invariant topology of a nonlinear sparse gene regulatory network using fully Bayesian spline autoregression Biostatistics 2011; doi: 10.1093/biostatistics/kxr009

### See Also

`NonLinearNet`, `LinearNet`, `ReplicatesNet_student` , `ReplicatesNet_gauss` .

### Examples

      #############################################
      ## Run inference using one chain
      #############################################
      # Load A. thaliana circadian clock ODE generated data
      data(Athaliana_ODE)
      # Folder where raw runs will be kept and analysed
      output.folder <- paste(tempdir(), "/Example_LinearNet", sep="")
      # Run network inference, place raw results in output.folder
      # Run just one chain for example purpose
      LinearNet(output.folder, Athaliana_ODE, chains = 1)

      ###########################
      ## Read chain
      ###########################
      chain1 <- read.chain(output.folder, 1)

[Package GRENITS version 1.46.0 Index]