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 |
coerce-method | Container for XDE parameters |
coerce-method | Container class for storing options of the Bayesian hierarchical model |
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 |
ExpressionSetList-methods | Methods for ExpressionSetList |
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 |
Parameters-class | Container for XDE parameters |
pca-method | A class for containing a list of ExpressionSets |
pData-method | A class for containing a list of ExpressionSets |
phenotype | Methods for ExpressionSetList |
phenotype-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 | Container for XDE parameters |
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 | Container for XDE parameters |
$-method | Class for storing output from the Bayesian model |
$<--method | Container for XDE parameters |
.standardizedDelta-method | Class for storing output from the Bayesian model |
[-method | A class for containing a list of ExpressionSets |
[-method | Methods for ExpressionSetList |
[[-method | Container for XDE parameters |
[[<--method | Container for XDE parameters |