# XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression

## Documentation for package ‘XDE’ version 1.0.0

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

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

## -- B --

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

## -- C --

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

## -- D --

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

## -- E --

empiricalStart | Empirical starting values for the MCMC
expressionSetList | Example of ExpressionSetList
ExpressionSetList-class | A class for containing a list of ExpressionSets

## -- F --

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

## -- G --

geneCenter | Center the expression values for each gene in a study to zero
geneCenter,ExpressionSetList-method | A class for containing a list of ExpressionSets

## -- H --

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

## -- I --

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

## -- L --

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

## -- N --

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

## -- O --

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

## -- P --

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

## -- S --

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

## -- T --

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

## -- U --

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

## -- X --

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

## -- Z --

zeroNu | Option for not modeling Nu
zeroNu,ExpressionSetList-method | A class for containing a list of ExpressionSets

## -- misc --

[,ExpressionSetList-method | A class for containing a list of ExpressionSets