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B C D E F G H I L N O P S T U X Z misc
| bayesianEffectSize | Class for storing output from the Bayesian model |
| bayesianEffectSize-method | Class for storing output from the Bayesian model |
| bayesianEffectSize<- | Class for storing output from the Bayesian model |
| bayesianEffectSize<--method | Class for storing output from the Bayesian model |
| burnin | Indicator for running a MCMC burnin |
| burnin-method | Container class for storing options of the Bayesian hierarchical model |
| burnin<- | Indicator for running a MCMC burnin |
| burnin<--method | Container class for storing options of the Bayesian hierarchical model |
| calculateBayesianEffectSize | Class for storing output from the Bayesian model |
| calculateBayesianEffectSize-method | Class for storing output from the Bayesian model |
| calculatePosteriorAvg | Calculate the posterior average for indicators of concordant and discordant differential expression |
| calculatePosteriorAvg-method | Class for storing output from the Bayesian model |
| coerce-method | A class for containing a list of ExpressionSets |
| dim-method | A class for containing a list of ExpressionSets |
| directory | Class for storing output from the Bayesian model |
| directory-method | Class for storing output from the Bayesian model |
| directory-method | Container class for storing options of the Bayesian hierarchical model |
| directory<- | Container class for storing options of the Bayesian hierarchical model |
| directory<--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-method | A class for containing a list of ExpressionSets |
| featureNames-method | Class for storing output from the Bayesian model |
| firstMcmc | Values for the first MCMC iteration |
| firstMcmc-method | Container class for storing options of the Bayesian hierarchical model |
| firstMcmc<- | Values for the first MCMC iteration |
| firstMcmc<--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-method | A class for containing a list of ExpressionSets |
| hyperparameters | Accessor for hyperparameters of the Bayesian model |
| hyperparameters-method | Container class for storing options of the Bayesian hierarchical model |
| hyperparameters<- | Accessor for hyperparameters of the Bayesian model |
| hyperparameters<--method | Container class for storing options of the Bayesian hierarchical model |
| initialize-method | Class for storing output from the Bayesian model |
| initialize-method | Container class for storing options of the Bayesian hierarchical model |
| iterations | Number of MCMC iterations |
| iterations-method | Class for storing output from the Bayesian model |
| iterations-method | Container class for storing options of the Bayesian hierarchical model |
| iterations<- | Number of MCMC iterations |
| iterations<--method | Container class for storing options of the Bayesian hierarchical model |
| lapply-method | A class for containing a list of ExpressionSets |
| lastMcmc | MCMC values for the last iteration |
| lastMcmc-method | Class for storing output from the Bayesian model |
| lastMcmc<- | MCMC values for the last iteration |
| nrow-method | A class for containing a list of ExpressionSets |
| nrow-method | Class for storing output from the Bayesian model |
| nSamples | A class for containing a list of ExpressionSets |
| nSamples-method | A class for containing a list of ExpressionSets |
| output | Options for storing results of the MCMC chains |
| output-method | Class for storing output from the Bayesian model |
| output-method | Container class for storing options of the Bayesian hierarchical model |
| output<- | Options for storing results of the MCMC chains |
| output<--method | Container class for storing options of the Bayesian hierarchical model |
| pairs-method | pairs function for high-throughput data |
| pairs-methods | pairs function for high-throughput data |
| pca-method | A class for containing a list of ExpressionSets |
| pData-method | A class for containing a list of ExpressionSets |
| phenotypeLabel | Container class for storing options of the Bayesian hierarchical model |
| phenotypeLabel-method | Container class for storing options of the Bayesian hierarchical model |
| phenotypeLabel<- | Container class for storing options of the Bayesian hierarchical model |
| phenotypeLabel<--method | Container class for storing options of the Bayesian hierarchical model |
| plot-method | Class for storing output from the Bayesian model |
| posteriorAvg | Accessor and replacement methods for posterior averages of differential expression |
| posteriorAvg-method | Class for storing output from the Bayesian model |
| posteriorAvg<- | Accessor and replacement methods for posterior averages of differential expression |
| posteriorAvg<--method | Class for storing output from the Bayesian model |
| savedIterations | Container class for storing options of the Bayesian hierarchical model |
| savedIterations-method | Container class for storing options of the Bayesian hierarchical model |
| seed | Seed for the MCMC |
| seed-method | Class for storing output from the Bayesian model |
| seed-method | Container class for storing options of the Bayesian hierarchical model |
| seed<- | Seed for the MCMC |
| seed<--method | Container class for storing options of the Bayesian hierarchical model |
| show-method | Class for storing output from the Bayesian model |
| show-method | Container class for storing options of the Bayesian hierarchical model |
| showIterations | Container class for storing options of the Bayesian hierarchical model |
| showIterations-method | Container class for storing options of the Bayesian hierarchical model |
| showIterations<- | Container class for storing options of the Bayesian hierarchical model |
| showIterations<--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-method | A class for containing a list of ExpressionSets |
| studyCenter | Center the expression values in a study to zero |
| studyCenter-method | A class for containing a list of ExpressionSets |
| studyNames | Container class for storing options of the Bayesian hierarchical model |
| studyNames-method | Class for storing output from the Bayesian model |
| studyNames-method | Container class for storing options of the Bayesian hierarchical model |
| studyNames<- | Container class for storing options of the Bayesian hierarchical model |
| studyNames<--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-method | Container class for storing options of the Bayesian hierarchical model |
| thin<- | How often to write MCMC iterations to file |
| thin<--method | Container class for storing options of the Bayesian hierarchical model |
| tuning | Tuning parameters for Metropolis-Hastings proposals |
| tuning-method | Container class for storing options of the Bayesian hierarchical model |
| tuning<- | Tuning parameters for Metropolis-Hastings proposals |
| tuning<--method | Container class for storing options of the Bayesian hierarchical model |
| updates | Frequency of updating a parameter per MCMC iteration |
| updates-method | Container class for storing options of the Bayesian hierarchical model |
| updates<- | Frequency of updating a parameter per MCMC iteration |
| updates<--method | Container class for storing options of the Bayesian hierarchical model |
| 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-method | A class for containing a list of ExpressionSets |
| $ | Class for storing output from the Bayesian model |
| $-method | Class for storing output from the Bayesian model |
| .integrativeCorrelationFilter-method | A class for containing a list of ExpressionSets |
| .standardizedDelta-method | Class for storing output from the Bayesian model |
| [-method | A class for containing a list of ExpressionSets |