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

## Documentation for package ‘XDE’ version 2.0.0

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.
- Package NEWS.

## Help Pages

B C D E F G H I L N O P R S T U X Z misc

## -- B --

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

## -- C --

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

## -- D --

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

## -- E --

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

## -- F --

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

## -- G --

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

## -- H --

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

## -- I --

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

## -- L --

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

## -- N --

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

## -- O --

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

## -- P --

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

## -- R --

rupdateAlpha_MRF | R interface to MCMC updates in C
rupdateANu | R interface to MCMC updates in C
rupdateBDDelta | R interface to MCMC updates in C
rupdateBetag_MRF | R interface to MCMC updates in C
rupdateBeta_MRF | R interface to MCMC updates in C
rupdateC2 | R interface to MCMC updates in C
rupdateC2DDelta | R interface to MCMC updates in C
rupdateDDelta | R interface to MCMC updates in C
rupdateDeltaDDelta | R interface to MCMC updates in C
rupdateDeltaDDelta_MRF | R interface to MCMC updates in C
rupdateGamma2 | R interface to MCMC updates in C
rupdateGamma2Nu | R interface to MCMC updates in C
rupdateL | R interface to MCMC updates in C
rupdateLambda | R interface to MCMC updates in C
rupdateLambdaPhi | R interface to MCMC updates in C
rupdateLSigma2 | R interface to MCMC updates in C
rupdateNu | R interface to MCMC updates in C
rupdatePhi | R interface to MCMC updates in C
rupdateRC2 | R interface to MCMC updates in C
rupdateRDDelta | R interface to MCMC updates in C
rupdateRhoGamma2 | R interface to MCMC updates in C
rupdateRhoNu | R interface to MCMC updates in C
rupdateSigma2 | R interface to MCMC updates in C
rupdateT | R interface to MCMC updates in C
rupdateTau2RDDelta | R interface to MCMC updates in C
rupdateTau2RhoNu | R interface to MCMC updates in C
rupdateTheta | R interface to MCMC updates in C
rupdateThetaPhi | R interface to MCMC updates in C
rupdateTSigma2 | R interface to MCMC updates in C
rupdateXi | R interface to MCMC updates in C

## -- S --

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

## -- T --

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

## -- U --

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

## -- X --

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-method | A class for containing a list of ExpressionSets

## -- misc --

$ | 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
.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
[[-method | Container for XDE parameters
[[<--method | Container for XDE parameters