XdeParameter-class {XDE} | R Documentation

## Container class for storing options of the Bayesian hierarchical model

### Description

This class contains initial values for the first iteration of the MCMC, options for saving MCMC chains, options for changing the tuning parameters of the Metropolis-Hastings algorithm, options for changing hyperparameters from their defaults, etc.

### Objects from the Class

Objects can be created by calls of the form `new("XdeParameter", esetList, updates, tuning, hyperparameters, output, iterations, burnin, seed, randomSeed, genes, studies, firstMcmc, specifiedInitialValues, directory, phenotypeLabel, showIterations, verbose, studyNames)`.

### Slots

`updates`:
  Object of class `numeric`. The frequency of updates for each iteration of the chain.
`tuning`:
  Object of class `numeric`. Tuning parameters for the Metropolis-Hastings proposals
`hyperparameters`:
  Object of class `numeric`. Hyperparameters for the Bayesian hierarchical model
`output`:
  Object of class `numeric`. Indicator for whether to save the MCMC chain to file. If the value is zero, the chain is not saved.
`iterations`:
  Object of class `numeric`. The total number of MCMC iterations.
`burnin`:
  Object of class `logical`. If set to FALSE, by default none of the chains will be saved (called for its side-effect of setting the output to zero for each parameter).
`notes`:
  Object of class `character`.
`firstMcmc`:
  Object of class `environment`. Values for the first iteration of the MCMC
`showIterations`:
  Object of class `logical`. Whether to show the MCMC iteration when fitting the model
`specifiedInitialValues`:
  Object of class `logical`. If TRUE (the default), the values stored in `firstMcmc` will be used for the first iteration of the MCMC.
`directory`:
  Object of class `character`. Specifies where to write the log files
`phenotypeLabel`:
  Object of class `character`. The name of the binary covariate used for differential expression
`verbose`:
  Object of class `logical`
`studyNames`:
  Object of class `character`. Names of the datasets

### Methods

burnin
  `signature(object = "XdeParameter")` logical. See `burnin`
burnin<-
  `signature(object = "XdeParameter", value = "logical")` logical. See `burnin`
directory
  `signature(object = "XdeParameter")` character string giving the path or relative path to store log files from the MCMC chain
directory<-
  `signature(object = "XdeParameter")`Path to store log files.
firstMcmc
  `signature(object = "XdeParameter")` See `firstMcmc`
firstMcmc<-
  `signature(object = "XdeParameter", value = "environment")`
firstMcmc<-
  `signature(object = "XdeParameter", value = "list")`
hyperparameters
  `signature(object = "XdeParameter")` See the XdeParameterClass vignette
hyperparameters<-
  `signature(object = "XdeParameter")` See the XdeParameterClass vignette
initialize
  `signature(.Object = "XdeParameter")` Method for initializing an instance of the class. The default values provided work well in most cases.
iterations
  `signature(object = "XdeParameter")` Accessor for the total number of MCMC iterations to run
iterations<-
  `signature(object = "XdeParameter", value = numeric)` The replacement method is useful for setting a different number of iterations.
iterations<-
  `signature(object = "XdeParameter", value = "integer")`
output
  `signature(object = "XdeParameter")` See also `output`. This method is also defined for class `XdeMcmc`
output<-
  `signature(object = "XdeParameter")` See also `output`
phenotypeLabel
  `signature(object = "XdeParameter")` The name of a binary covariate present in each study
phenotypeLabel<-
  `signature(object = "XdeParameter", value = "character")`
savedIterations
  `signature(object = "XdeParameter")` The number of MCMC iterations written to file. It is the value of the total number of iterations divided by the thinning parameter. See also `output`
seed
  `signature(object = "XdeParameter")` See `seed`
seed<-
  `signature(object = "XdeParameter", value="integer")` Replacement method. See also `seed`.
show
  `signature(object = "XdeParameter")` Produces a short summary of objects that are instances of the `XdeParameter` class
showIterations
  `signature(object = "XdeParameter")` logical
showIterations<-
  `signature(object = "XdeParameter")`
studyNames
  `signature(object = "XdeParameter")` Names of the high-throughput gene expression studies
studyNames<-
  `signature(object = "XdeParameter")`
thin
  `signature(x = "XdeParameter")` See `output` and `thin`
thin<-
  `signature(x = "XdeParameter", value = numeric)` See `thin`
tuning
  `signature(object = "XdeParameter")` See also `tuning`
tuning<-
  `signature(object = "XdeParameter")`
updates
  `signature(object = "XdeParameter")` See also `updates`
updates<-
  `signature(object = "XdeParameter")`

### Author(s)

R. Scharpf

### References

R. Scharpf

### See Also

`ExpressionSetList-class`

### Examples

    showClass("XdeParameter")
    ##See the XdeParameterClass vignette

[Package XDE version 1.0.0 Index]