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<- | 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<- | Indicator for running a MCMC burnin |
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 |
dim,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<- | 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<- | Values for the first MCMC iteration |
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<- | Accessor for hyperparameters of the Bayesian 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<- | Number of MCMC iterations |
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 |
lastMcmc<- | MCMC values for the last iteration |
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<- | Options for storing results of the MCMC chains |
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<- | 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,ANY-method | Class for storing output from the Bayesian 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<- | Accessor and replacement methods for posterior averages of differential expression |
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<- | Seed for the MCMC |
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<- | 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<- | 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<- | How often to write MCMC iterations to file |
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<- | Tuning parameters for Metropolis-Hastings proposals |
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<- | Frequency of updating a parameter per MCMC iteration |
updates<-,XdeParameter-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,ExpressionSetList-method | A class for containing a list of ExpressionSets |
[,ExpressionSetList-method | A class for containing a list of ExpressionSets |