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
.integrativeCorrelationFilter,ExpressionSetList-method Man page
.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 April 29, 2020, 3:32 a.m.