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B C D E F G H I L N O P S T U X Z misc
| $ | Class for storing output from the Bayesian model |
| $,XdeMcmc-method | Class for storing output from the Bayesian model |
| .integrativeCorrelationFilter,ExpressionSetList-method | A class for containing a list of ExpressionSets |
| .standardizedDelta,XdeMcmc-method | Class for storing output from the Bayesian model |
| bayesianEffectSize | Class for storing output from the Bayesian model |
| bayesianEffectSize,XdeMcmc-method | Class for storing output from the Bayesian model |
| bayesianEffectSize<-,XdeMcmc,matrix-method | Class for storing output from the Bayesian model |
| burnin | Indicator for running a MCMC burnin |
| burnin,XdeParameter-method | Container class for storing options of the Bayesian hierarchical model |
| burnin<-,XdeParameter,logical-method | Container class for storing options of the Bayesian hierarchical model |
| calculateBayesianEffectSize | Class for storing output from the Bayesian model |
| calculateBayesianEffectSize,XdeMcmc-method | Class for storing output from the Bayesian model |
| calculatePosteriorAvg | Calculate the posterior average for indicators of concordant and discordant differential expression |
| calculatePosteriorAvg,XdeMcmc-method | Class for storing output from the Bayesian model |
| coerce,list,ExpressionSetList-method | A class for containing a list of ExpressionSets |
| directory | Class for storing output from the Bayesian model |
| directory,XdeMcmc-method | Class for storing output from the Bayesian model |
| directory,XdeParameter-method | Container class for storing options of the Bayesian hierarchical model |
| directory<-,XdeParameter-method | Container class for storing options of the Bayesian hierarchical model |
| empiricalStart | Empirical starting values for the MCMC |
| expressionSetList | Example of ExpressionSetList |
| ExpressionSetList-class | A class for containing a list of ExpressionSets |
| featureNames,ExpressionSetList-method | A class for containing a list of ExpressionSets |
| featureNames,XdeMcmc-method | Class for storing output from the Bayesian model |
| firstMcmc | Values for the first MCMC iteration |
| firstMcmc,XdeParameter-method | Container class for storing options of the Bayesian hierarchical model |
| firstMcmc<-,XdeParameter,environment-method | Container class for storing options of the Bayesian hierarchical model |
| firstMcmc<-,XdeParameter,list-method | Container class for storing options of the Bayesian hierarchical model |
| geneCenter | Center the expression values for each gene in a study to zero |
| geneCenter,ExpressionSetList-method | A class for containing a list of ExpressionSets |
| hyperparameters | Accessor for hyperparameters of the Bayesian model |
| hyperparameters,XdeParameter-method | Container class for storing options of the Bayesian hierarchical model |
| hyperparameters<-,XdeParameter-method | Container class for storing options of the Bayesian hierarchical model |
| initialize,XdeMcmc-method | Class for storing output from the Bayesian model |
| initialize,XdeParameter-method | Container class for storing options of the Bayesian hierarchical model |
| iterations | Number of MCMC iterations |
| iterations,XdeMcmc-method | Class for storing output from the Bayesian model |
| iterations,XdeParameter-method | Container class for storing options of the Bayesian hierarchical model |
| iterations<-,XdeParameter,integer-method | Container class for storing options of the Bayesian hierarchical model |
| iterations<-,XdeParameter,numeric-method | Container class for storing options of the Bayesian hierarchical model |
| lapply,ExpressionSetList-method | A class for containing a list of ExpressionSets |
| lastMcmc | MCMC values for the last iteration |
| lastMcmc,XdeMcmc-method | Class for storing output from the Bayesian model |
| nrow,ExpressionSetList-method | A class for containing a list of ExpressionSets |
| nrow,XdeMcmc-method | Class for storing output from the Bayesian model |
| nSamples | A class for containing a list of ExpressionSets |
| nSamples,ExpressionSetList-method | A class for containing a list of ExpressionSets |
| output | Options for storing results of the MCMC chains |
| output,XdeMcmc-method | Class for storing output from the Bayesian model |
| output,XdeParameter-method | Container class for storing options of the Bayesian hierarchical model |
| output<-,XdeParameter-method | Container class for storing options of the Bayesian hierarchical model |
| pairs,data.frame-method | pairs function for high-throughput data |
| pairs,matrix-method | pairs function for high-throughput data |
| pairs-methods | pairs function for high-throughput data |
| pca,ExpressionSetList-method | A class for containing a list of ExpressionSets |
| pData,ExpressionSetList-method | A class for containing a list of ExpressionSets |
| phenotypeLabel | Container class for storing options of the Bayesian hierarchical model |
| phenotypeLabel,XdeParameter-method | Container class for storing options of the Bayesian hierarchical model |
| phenotypeLabel<-,XdeParameter,character-method | Container class for storing options of the Bayesian hierarchical model |
| plot,XdeMcmc-method | Class for storing output from the Bayesian model |
| posteriorAvg | Accessor and replacement methods for posterior averages of differential expression |
| posteriorAvg,XdeMcmc-method | Class for storing output from the Bayesian model |
| posteriorAvg<-,XdeMcmc,matrix-method | Class for storing output from the Bayesian model |
| savedIterations | Container class for storing options of the Bayesian hierarchical model |
| savedIterations,XdeParameter-method | Container class for storing options of the Bayesian hierarchical model |
| seed | Seed for the MCMC |
| seed,XdeMcmc-method | Class for storing output from the Bayesian model |
| seed,XdeParameter-method | Container class for storing options of the Bayesian hierarchical model |
| seed<-,XdeParameter,integer-method | Container class for storing options of the Bayesian hierarchical model |
| seed<-,XdeParameter,numeric-method | Container class for storing options of the Bayesian hierarchical model |
| show,XdeMcmc-method | Class for storing output from the Bayesian model |
| show,XdeParameter-method | Container class for storing options of the Bayesian hierarchical model |
| showIterations | Container class for storing options of the Bayesian hierarchical model |
| showIterations,XdeParameter-method | Container class for storing options of the Bayesian hierarchical model |
| showIterations<-,XdeParameter-method | Container class for storing options of the Bayesian hierarchical model |
| ssStatistic | Calculate single study estimates of effect size |
| standardizeSamples | Centers the genes at zero and standardizes the samples to have variance 1 |
| standardizeSamples,ExpressionSetList-method | A class for containing a list of ExpressionSets |
| studyCenter | Center the expression values in a study to zero |
| studyCenter,ExpressionSetList-method | A class for containing a list of ExpressionSets |
| studyNames | Container class for storing options of the Bayesian hierarchical model |
| studyNames,XdeMcmc-method | Class for storing output from the Bayesian model |
| studyNames,XdeParameter-method | Container class for storing options of the Bayesian hierarchical model |
| studyNames<-,XdeParameter-method | Container class for storing options of the Bayesian hierarchical model |
| symbolsInteresting | Useful for changing the look of pairs plots to emphasize concordant or discordant genes |
| thin | How often to write MCMC iterations to file |
| thin,XdeParameter-method | Container class for storing options of the Bayesian hierarchical model |
| thin<-,XdeParameter,numeric-method | Container class for storing options of the Bayesian hierarchical model |
| tuning | Tuning parameters for Metropolis-Hastings proposals |
| tuning,XdeParameter-method | Container class for storing options of the Bayesian hierarchical model |
| tuning<-,XdeParameter-method | Container class for storing options of the Bayesian hierarchical model |
| updates | Frequency of updating a parameter per MCMC iteration |
| updates,XdeParameter-method | Container class for storing options of the Bayesian hierarchical model |
| updates<-,XdeParameter-method | Container class for storing options of the Bayesian hierarchical model |
| xapply | An lapply for ExpressionSetList |
| xapply,ExpressionSetList-method | A class for containing a list of ExpressionSets |
| xde | Fit the Bayesian hierarchical model for cross-study differential gene expression |
| XdeMcmc-class | Class for storing output from the Bayesian model |
| XdeParameter-class | Container class for storing options of the Bayesian hierarchical model |
| xmcmc | Object of class XdeMcmc |
| xsScores | Alternative cross-study scores of differential expression |
| zeroNu | Option for not modeling Nu |
| zeroNu,ExpressionSetList-method | A class for containing a list of ExpressionSets |
| [,ExpressionSetList-method | A class for containing a list of ExpressionSets |