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

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(XDE)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Welcome to XDE version 2.18.0
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/XDE/XdeParameter-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: XdeParameter-class
> ### Title: Container class for storing options of the Bayesian hierarchical
> ###   model
> ### Aliases: XdeParameter-class burnin,XdeParameter-method
> ###   burnin<-,XdeParameter,logical-method
> ###   coerce,XdeParameter,Params-method directory,XdeParameter-method
> ###   directory<- directory<-,XdeParameter-method
> ###   firstMcmc,XdeParameter-method
> ###   firstMcmc<-,XdeParameter,environment-method
> ###   firstMcmc<-,XdeParameter,list-method
> ###   hyperparameters,XdeParameter-method
> ###   hyperparameters<-,XdeParameter-method initialize,XdeParameter-method
> ###   iterations,XdeParameter-method
> ###   iterations<-,XdeParameter,numeric-method
> ###   iterations<-,XdeParameter,integer-method output,XdeParameter-method
> ###   output<-,XdeParameter-method phenotypeLabel phenotypeLabel<-
> ###   phenotypeLabel,XdeParameter-method
> ###   phenotypeLabel<-,XdeParameter,character-method savedIterations
> ###   savedIterations,XdeParameter-method seed,XdeParameter-method
> ###   seed<-,XdeParameter,integer-method seed<-,XdeParameter,numeric-method
> ###   show,XdeParameter-method showIterations showIterations<-
> ###   showIterations,XdeParameter-method
> ###   showIterations<-,XdeParameter-method studyNames studyNames<-
> ###   studyNames,XdeParameter-method studyNames<-,XdeParameter-method
> ###   thin,XdeParameter-method thin<-,XdeParameter,numeric-method
> ###   tuning,XdeParameter-method tuning<-,XdeParameter-method
> ###   updates,XdeParameter-method updates<-,XdeParameter-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> showClass("XdeParameter")
Class "XdeParameter" [package "XDE"]

Slots:
                                                                           
Name:                 updates                 tuning        hyperparameters
Class:                numeric                numeric                numeric
                                                                           
Name:                  output             iterations                 burnin
Class:                numeric                numeric                logical
                                                                           
Name:                    seed                  notes              firstMcmc
Class:                integer              character            environment
                                                                           
Name:          showIterations specifiedInitialValues              directory
Class:                logical                logical              character
                                                                           
Name:          phenotypeLabel                verbose             studyNames
Class:              character                logical              character
                             
Name:               one.delta
Class:                logical
> ##See the XdeParameterClass vignette
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>