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

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Documentation for package ‘XDE’ version 2.53.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

B C D E F G H I L N O P 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

-- 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
.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