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

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Search the XDE package
Vignettes
Functions
206
Source code
24
Man pages
29
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XDE: XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression
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API

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

Global functions
$ Man page
$,Parameters-method Man page
$,XdeMcmc-method Man page
$<-,Parameters-method Man page
.chainInitialize Source code
.goodnessOfFit Source code
.hyperparametersDefault Source code
.onAttach Source code
.onUnload Source code
.outputDefault Source code
.parameterNames Source code
.permuteClassLabels Source code
.permutePhenotype Source code
.standardizedDelta,XdeMcmc-method Man page
.tuningDefault Source code
.updatesDefault Source code
.xdeparameterlist Source code
ExpressionSetList-class Man page
ExpressionSetList-methods Man page
Parameters Source code
Parameters-class Man page
ParametersC Source code
ParametersD Source code
ParametersMII Source code
XdeMcmc-class Man page
XdeParameter-class Man page
[,ExpressionSetList,ANY,ANY,ANY-method Man page
[,ExpressionSetList-method Man page Man page
[[,Parameters-method Man page
[[<-,Parameters-method Man page
bayesianEffectSize Man page
bayesianEffectSize,XdeMcmc-method Man page
bayesianEffectSize<- Man page
bayesianEffectSize<-,XdeMcmc,matrix-method Man page
burnin Man page
burnin,XdeParameter-method Man page
burnin<- Man page
burnin<-,XdeParameter,logical-method Man page
calculateBayesianEffectSize Man page
calculateBayesianEffectSize,XdeMcmc-method Man page
calculatePosteriorAvg Man page Source code
calculatePosteriorAvg,XdeMcmc-method Man page
coerce,XdeParameter,Parameters-method Man page
coerce,XdeParameter,Params-method Man page
coerce,list,ExpressionSetList-method Man page Man page
computeGOF Source code
dim,ExpressionSetList-method Man page Man page
directory Man page
directory,XdeMcmc-method Man page
directory,XdeParameter-method Man page
directory<- Man page
directory<-,XdeParameter-method Man page
empiricalStart Man page Source code
expressionSetList Man page
featureNames,ExpressionSetList-method Man page
featureNames,XdeMcmc-method Man page
firstMcmc Man page
firstMcmc,XdeParameter-method Man page
firstMcmc<- Man page
firstMcmc<-,XdeParameter,environment-method Man page
firstMcmc<-,XdeParameter,list-method Man page
geneCenter Man page
geneCenter,ExpressionSetList-method Man page
hyperparameters Man page
hyperparameters,XdeParameter-method Man page
hyperparameters<- Man page
hyperparameters<-,XdeParameter-method Man page
initialize,XdeMcmc-method Man page
initialize,XdeParameter-method Man page
iterations Man page
iterations,XdeMcmc-method Man page
iterations,XdeParameter-method Man page
iterations<- Man page
iterations<-,XdeParameter,integer-method Man page
iterations<-,XdeParameter,numeric-method Man page
lapply,ExpressionSetList-method Man page Man page
lastMcmc Man page
lastMcmc,XdeMcmc-method Man page
lastMcmc<- Man page
makeSigma Source code
modelA_B_MIupdates Source code
nSamples Man page
nSamples,ExpressionSetList-method Man page
nrow,ExpressionSetList-method Man page
nrow,XdeMcmc-method Man page
output Man page
output,XdeMcmc-method Man page
output,XdeParameter-method Man page
output<- Man page
output<-,XdeParameter-method Man page
pData,ExpressionSetList-method Man page
pairs,data.frame-method Man page
pairs,matrix-method Man page
pairs-methods Man page
pca,ExpressionSetList-method Man page
phenotype Man page
phenotype,ExpressionSetList,character-method Man page
phenotypeLabel Man page
phenotypeLabel,XdeParameter-method Man page
phenotypeLabel<- Man page
phenotypeLabel<-,XdeParameter,character-method Man page
plot,XdeMcmc,ANY-method Man page
plot,XdeMcmc-method Man page
posteriorAvg Man page
posteriorAvg,XdeMcmc-method Man page
posteriorAvg<- Man page
posteriorAvg<-,XdeMcmc,matrix-method Man page
rupdateANu Source code
rupdateAlpha Source code
rupdateAlpha_onedelta Source code
rupdateBDDelta Source code
rupdateBDDeltaStar_HyperInverseWishart Source code
rupdateBeta Source code
rupdateBeta_onedelta Source code
rupdateBetag Source code
rupdateC2 Source code
rupdateC2DDelta Source code
rupdateDDelta Source code
rupdateDDeltaStar_HyperInverseWishart Source code
rupdateDelta Source code
rupdateDeltaDDelta Source code
rupdateDeltaDDelta_MRF2 Source code
rupdateDelta_MRF2 Source code
rupdateGamma2 Source code
rupdateGamma2Nu Source code
rupdateL Source code
rupdateLSigma2 Source code
rupdateLSigma2_HyperInverseWishart Source code
rupdateLambda Source code
rupdateLambdaPhi Source code
rupdateNu Source code
rupdateOmega_HyperInverseWishart Source code
rupdatePhi Source code
rupdateRC2 Source code
rupdateRDDelta Source code
rupdateRDDeltaStar_HyperInverseWishart Source code
rupdateRhoGamma2 Source code
rupdateRhoNu Source code
rupdateSigma2 Source code
rupdateSigma2_HyperInverseWishart Source code
rupdateT Source code
rupdateTSigma2 Source code
rupdateTSigma2_HyperInverseWishart Source code
rupdateTau2RDDelta Source code
rupdateTau2RDDeltaStar_HyperInverseWishart Source code
rupdateTau2RhoNu Source code
rupdateTheta Source code
rupdateThetaPhi Source code
rupdateXi Source code
savedIterations Man page
savedIterations,XdeParameter-method Man page
seed Man page
seed,XdeMcmc-method Man page
seed,XdeParameter-method Man page
seed<- Man page
seed<-,XdeParameter,integer-method Man page
seed<-,XdeParameter,numeric-method Man page
show,Parameters-method Man page
show,XdeMcmc-method Man page
show,XdeParameter-method Man page
showIterations Man page
showIterations,XdeParameter-method Man page
showIterations<- Man page
showIterations<-,XdeParameter-method Man page
ssStatistic Man page Source code
standardizeSamples Man page
standardizeSamples,ExpressionSetList-method Man page
startingValues Source code
studyCenter Man page
studyCenter,ExpressionSetList-method Man page
studyNames Man page
studyNames,XdeMcmc-method Man page
studyNames,XdeParameter-method Man page
studyNames<- Man page
studyNames<-,XdeParameter-method Man page
symbolsInteresting Man page Source code
thin Man page
thin,XdeParameter-method Man page
thin<- Man page
thin<-,XdeParameter,numeric-method Man page
tuning Man page
tuning,XdeParameter-method Man page
tuning<- Man page
tuning<-,XdeParameter-method Man page
updateMissing Source code
updates Man page
updates,XdeParameter-method Man page
updates<- Man page
updates<-,XdeParameter-method Man page
validityMethod Source code
xde Man page Source code
xdeFit Source code
xmcmc Man page
xsScores Man page Source code
zeroNu Man page
zeroNu,ExpressionSetList-method Man page
XDE documentation built on Nov. 8, 2020, 5:02 p.m.

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