R Graphical Manual

Last data update: 2014.03.03

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Results 1 - 10 of 27 found.
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ExpressionSetList-class (Package: XDE) : A class for containing a list of ExpressionSets

Each element in the list must be a valid ExpressionSet. The featureNames must be identical for each ExpressionSet.

● Data Source: BioConductor
● Keywords: classes
● Alias: .integrativeCorrelationFilter,ExpressionSetList-method, ExpressionSetList-class, [,ExpressionSetList-method, coerce,list,ExpressionSetList-method, dim,ExpressionSetList-method, featureNames,ExpressionSetList-method, geneCenter,ExpressionSetList-method, lapply,ExpressionSetList-method, nSamples, nSamples,ExpressionSetList-method, nrow,ExpressionSetList-method, pData,ExpressionSetList-method, pca,ExpressionSetList-method, phenotype,ExpressionSetList,character-method, standardizeSamples,ExpressionSetList-method, studyCenter,ExpressionSetList-method, zeroNu,ExpressionSetList-method
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ExpressionSetList-methods (Package: XDE) : Methods for ExpressionSetList

Methods for objects of class ExpressionSetList.

● Data Source: BioConductor
● Keywords: manip, methods
● Alias: ExpressionSetList-methods
● 0 images

Parameters-class (Package: XDE) : Container for XDE parameters

Container for XDE parameters

● Data Source: BioConductor
● Keywords: classes
● Alias: $,Parameters-method, $<-,Parameters-method, Parameters-class, [[,Parameters-method, [[<-,Parameters-method, coerce,XdeParameter,Parameters-method, show,Parameters-method
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XdeMcmc-class (Package: XDE) : Class for storing output from the Bayesian model

Stores output, including the last iteration of the MCMC.

● Data Source: BioConductor
● Keywords: classes
● Alias: $, $,XdeMcmc-method, .standardizedDelta,XdeMcmc-method, XdeMcmc-class, bayesianEffectSize, bayesianEffectSize,XdeMcmc-method, bayesianEffectSize<-, bayesianEffectSize<-,XdeMcmc,matrix-method, calculateBayesianEffectSize, calculateBayesianEffectSize,XdeMcmc-method, calculatePosteriorAvg,XdeMcmc-method, directory, directory,XdeMcmc-method, featureNames,XdeMcmc-method, initialize,XdeMcmc-method, iterations,XdeMcmc-method, lastMcmc,XdeMcmc-method, nrow,XdeMcmc-method, output,XdeMcmc-method, plot,XdeMcmc,ANY-method, plot,XdeMcmc-method, posteriorAvg,XdeMcmc-method, posteriorAvg<-,XdeMcmc,matrix-method, seed,XdeMcmc-method, show,XdeMcmc-method, studyNames,XdeMcmc-method
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XdeParameter-class (Package: XDE) : Container class for storing options of the Bayesian hierarchical model

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.

● Data Source: BioConductor
● Keywords: classes
● Alias: 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,integer-method, iterations<-,XdeParameter,numeric-method, output,XdeParameter-method, output<-,XdeParameter-method, phenotypeLabel, phenotypeLabel,XdeParameter-method, phenotypeLabel<-, phenotypeLabel<-,XdeParameter,character-method, savedIterations, savedIterations,XdeParameter-method, seed,XdeParameter-method, seed<-,XdeParameter,integer-method, seed<-,XdeParameter,numeric-method, show,XdeParameter-method, showIterations, showIterations,XdeParameter-method, showIterations<-, showIterations<-,XdeParameter-method, studyNames, studyNames,XdeParameter-method, studyNames<-, studyNames<-,XdeParameter-method, thin,XdeParameter-method, thin<-,XdeParameter,numeric-method, tuning,XdeParameter-method, tuning<-,XdeParameter-method, updates,XdeParameter-method, updates<-,XdeParameter-method
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burnin (Package: XDE) : Indicator for running a MCMC burnin

When TRUE, log files from MCMC chains are not written to file. When FALSE, log files are written for every parameter by default.

● Data Source: BioConductor
● Keywords: methods
● Alias: burnin, burnin<-
● 0 images

calculatePosteriorAvg (Package: XDE) : Calculate the posterior average for indicators of concordant and

This function calculates the posterior average for indicators of concordant and discordant differential expression from the saved log files. See details.

● Data Source: BioConductor
● Keywords: manip
● Alias: calculatePosteriorAvg
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empiricalStart (Package: XDE) : Empirical starting values for the MCMC

Empirical starting values for the MCMC are based on data in objects of class ExpressionSetList

● Data Source: BioConductor
● Keywords: methods
● Alias: empiricalStart
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firstMcmc (Package: XDE) : Values for the first MCMC iteration

Accessor method for the values of the first MCMC iteration

● Data Source: BioConductor
● Keywords: methods
● Alias: firstMcmc, firstMcmc<-
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geneCenter (Package: XDE) : Center the expression values for each gene in a study to zero

Mean centers the genes for each study in a list

● Data Source: BioConductor
● Keywords: methods
● Alias: geneCenter
● 0 images