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

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Documentation for package ‘XDE’ version 2.26.0

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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
.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 Methods for ExpressionSetList
[[-method Container for XDE parameters
[[<--method Container for XDE parameters