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, seed, showIterations, verbose, studyNames, one.delta)`.

### 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

`seed`:

  Object of class `integer`. Seed used for simulating random numbers.

`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

`one.delta`:

  Logical. If TRUE, a gene is assumed to be differentially in all studies or none of the studies.

### 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 2.28.0 Index]