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

Multi-level model for cross-study detection of differential gene expression.

AuthorR.B. Scharpf, G. Parmigiani, A.B. Nobel, and H. Tjelmeland
Date of publicationNone
MaintainerRobert Scharpf <rscharpf@jhsph.edu>
LicenseLGPL-2
Version2.20.0

View on Bioconductor

Man pages

burnin: Indicator for running a MCMC burnin

calculatePosteriorAvg: Calculate the posterior average for indicators of concordant...

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

firstMcmc: Values for the first MCMC iteration

geneCenter: Center the expression values for each gene in a study to zero

hyperparameters: Accessor for hyperparameters of the Bayesian model

iterations: Number of MCMC iterations

lastMcmc: MCMC values for the last iteration

output: Options for storing results of the MCMC chains

pairs: pairs function for high-throughput data

Parameters-class: Container for XDE parameters

posteriorAvg: Accessor and replacement methods for posterior averages of...

seed: Seed for the MCMC

ssStatistic: Calculate single study estimates of effect size

standardizeSamples: Centers the genes at zero and standardizes the samples to...

studyCenter: Center the expression values in a study to zero

symbolsInteresting: Useful for changing the look of pairs plots to emphasize...

thin: How often to write MCMC iterations to file

tuning: Tuning parameters for Metropolis-Hastings proposals

updates: Frequency of updating a parameter per MCMC iteration

xde: Fit the Bayesian hierarchical model for cross-study...

XdeMcmc-class: Class for storing output from the Bayesian model

XdeParameter-class: Container class for storing options of the Bayesian...

xmcmc: Object of class XdeMcmc

xsScores: Alternative cross-study scores of differential expression

zeroNu: Option for not modeling Nu

Functions

$ Man page
bayesianEffectSize Man page
bayesianEffectSize<- Man page
bayesianEffectSize<-,XdeMcmc,matrix-method Man page
bayesianEffectSize,XdeMcmc-method Man page
burnin Man page
burnin<- Man page
burnin<-,XdeParameter,logical-method Man page
burnin,XdeParameter-method Man page
calculateBayesianEffectSize Man page
calculateBayesianEffectSize,XdeMcmc-method Man page
calculatePosteriorAvg Man page
calculatePosteriorAvg,XdeMcmc-method Man page
coerce,list,ExpressionSetList-method Man page
coerce,list,ExpressionSetList-method Man page
coerce,XdeParameter,Parameters-method Man page
coerce,XdeParameter,Params-method Man page
dim,ExpressionSetList-method Man page
dim,ExpressionSetList-method Man page
directory Man page
directory<- Man page
directory,XdeMcmc-method Man page
directory<-,XdeParameter-method Man page
directory,XdeParameter-method Man page
empiricalStart Man page
expressionSetList Man page
ExpressionSetList-class Man page
[,ExpressionSetList-method Man page
[,ExpressionSetList-method Man page
ExpressionSetList-methods Man page
featureNames,ExpressionSetList-method Man page
featureNames,XdeMcmc-method Man page
firstMcmc Man page
firstMcmc<- Man page
firstMcmc<-,XdeParameter,environment-method Man page
firstMcmc<-,XdeParameter,list-method Man page
firstMcmc,XdeParameter-method Man page
geneCenter Man page
geneCenter,ExpressionSetList-method Man page
hyperparameters Man page
hyperparameters<- Man page
hyperparameters<-,XdeParameter-method Man page
hyperparameters,XdeParameter-method Man page
initialize,XdeMcmc-method Man page
initialize,XdeParameter-method Man page
.integrativeCorrelationFilter,ExpressionSetList-method Man page
iterations Man page
iterations<- Man page
iterations,XdeMcmc-method Man page
iterations<-,XdeParameter,integer-method Man page
iterations,XdeParameter-method Man page
iterations<-,XdeParameter,numeric-method Man page
lapply,ExpressionSetList-method Man page
lapply,ExpressionSetList-method Man page
lastMcmc Man page
lastMcmc<- Man page
lastMcmc,XdeMcmc-method Man page
nrow,ExpressionSetList-method Man page
nrow,XdeMcmc-method Man page
nSamples Man page
nSamples,ExpressionSetList-method Man page
output Man page
output<- Man page
output,XdeMcmc-method Man page
output<-,XdeParameter-method Man page
output,XdeParameter-method Man page
pairs,data.frame-method Man page
pairs,matrix-method Man page
pairs-methods Man page
Parameters-class Man page
[[<-,Parameters-method Man page
[[,Parameters-method Man page
$<-,Parameters-method Man page
$,Parameters-method Man page
pca,ExpressionSetList-method Man page
pData,ExpressionSetList-method Man page
phenotype Man page
phenotype,ExpressionSetList,character-method Man page
phenotypeLabel Man page
phenotypeLabel<- Man page
phenotypeLabel<-,XdeParameter,character-method Man page
phenotypeLabel,XdeParameter-method Man page
plot,XdeMcmc,ANY-method Man page
plot,XdeMcmc-method Man page
posteriorAvg Man page
posteriorAvg<- Man page
posteriorAvg<-,XdeMcmc,matrix-method Man page
posteriorAvg,XdeMcmc-method Man page
savedIterations Man page
savedIterations,XdeParameter-method Man page
seed Man page
seed<- Man page
seed,XdeMcmc-method Man page
seed<-,XdeParameter,integer-method Man page
seed,XdeParameter-method Man page
seed<-,XdeParameter,numeric-method Man page
showIterations Man page
showIterations<- Man page
showIterations<-,XdeParameter-method Man page
showIterations,XdeParameter-method Man page
show,Parameters-method Man page
show,XdeMcmc-method Man page
show,XdeParameter-method Man page
ssStatistic Man page
.standardizedDelta,XdeMcmc-method Man page
standardizeSamples Man page
standardizeSamples,ExpressionSetList-method Man page
studyCenter Man page
studyCenter,ExpressionSetList-method Man page
studyNames Man page
studyNames<- Man page
studyNames,XdeMcmc-method Man page
studyNames<-,XdeParameter-method Man page
studyNames,XdeParameter-method Man page
symbolsInteresting Man page
thin Man page
thin<- Man page
thin,XdeParameter-method Man page
thin<-,XdeParameter,numeric-method Man page
tuning Man page
tuning<- Man page
tuning<-,XdeParameter-method Man page
tuning,XdeParameter-method Man page
updates Man page
updates<- Man page
updates<-,XdeParameter-method Man page
updates,XdeParameter-method Man page
xde Man page
XdeMcmc-class Man page
$,XdeMcmc-method Man page
XdeParameter-class Man page
xmcmc Man page
xsScores Man page
zeroNu Man page
zeroNu,ExpressionSetList-method Man page

Files

XDE/CHANGES
XDE/DESCRIPTION
XDE/NAMESPACE
XDE/NEWS
XDE/R
XDE/R/AllClasses.R XDE/R/AllGenerics.R XDE/R/RUpdates.R XDE/R/functions.R XDE/R/methods-ExpressionSet.R XDE/R/methods-ExpressionSetList.R XDE/R/methods-Parameters.R XDE/R/methods-XdeMcmc.R XDE/R/methods-XdeParameter.R XDE/R/methods-data.frame.R XDE/R/methods-matrix.R XDE/R/methods-mergeExpressionSet.R XDE/R/xde.R XDE/R/zzz.R
XDE/build
XDE/build/vignette.rds
XDE/data
XDE/data/.commands.R
XDE/data/.createLogFiles.R
XDE/data/expressionSetList.RData
XDE/data/xmcmc.RData
XDE/inst
XDE/inst/CITATION
XDE/inst/Test
XDE/inst/Test/DESCRIPTION
XDE/inst/Test/NAMESPACE
XDE/inst/Test/R
XDE/inst/Test/R/initializeParams.R
XDE/inst/Test/R/zzz.R
XDE/inst/Test/man
XDE/inst/Test/man/Test-package.Rd
XDE/inst/Test/src
XDE/inst/Test/src/Cholesky.cpp
XDE/inst/Test/src/Cholesky.h
XDE/inst/Test/src/Matrix.h
XDE/inst/Test/src/Matrix_v2.cpp
XDE/inst/Test/src/Matrix_v2.h
XDE/inst/Test/src/Potential.h
XDE/inst/Test/src/PotentialA.h
XDE/inst/Test/src/PotentialB.h
XDE/inst/Test/src/PotentialDDelta.h
XDE/inst/Test/src/PotentialDDeltag.h
XDE/inst/Test/src/PotentialDelta.h
XDE/inst/Test/src/PotentialDeltag.h
XDE/inst/Test/src/PotentialFunction.h
XDE/inst/Test/src/PotentialNu.h
XDE/inst/Test/src/PotentialNug.h
XDE/inst/Test/src/PotentialPhi.h
XDE/inst/Test/src/PotentialPhiqg.h
XDE/inst/Test/src/PotentialR.h
XDE/inst/Test/src/PotentialRho.h
XDE/inst/Test/src/PotentialSigma2.h
XDE/inst/Test/src/PotentialSigma2qg.h
XDE/inst/Test/src/PotentialSum.h
XDE/inst/Test/src/PotentialTau2.h
XDE/inst/Test/src/PotentialX.h
XDE/inst/Test/src/PotentialXi.h
XDE/inst/Test/src/PotentialXqg.h
XDE/inst/Test/src/PotentialZero.h
XDE/inst/Test/src/Potential_v2.cpp
XDE/inst/Test/src/Potential_v2.h
XDE/inst/Test/src/Random.h
XDE/inst/Test/src/Random_v2.cpp
XDE/inst/Test/src/Random_v2.h
XDE/inst/Test/src/Report.h
XDE/inst/Test/src/ReportA.h
XDE/inst/Test/src/ReportAcceptance.h
XDE/inst/Test/src/ReportB.h
XDE/inst/Test/src/ReportC2.h
XDE/inst/Test/src/ReportDDelta.h
XDE/inst/Test/src/ReportDelta.h
XDE/inst/Test/src/ReportDiffexpressed.h
XDE/inst/Test/src/ReportGamma2.h
XDE/inst/Test/src/ReportL.h
XDE/inst/Test/src/ReportLambda.h
XDE/inst/Test/src/ReportNu.h
XDE/inst/Test/src/ReportPhi.h
XDE/inst/Test/src/ReportPotential.h
XDE/inst/Test/src/ReportProbDelta.h
XDE/inst/Test/src/ReportR.h
XDE/inst/Test/src/ReportRho.h
XDE/inst/Test/src/ReportSigma2.h
XDE/inst/Test/src/ReportT.h
XDE/inst/Test/src/ReportTau2R.h
XDE/inst/Test/src/ReportTau2Rho.h
XDE/inst/Test/src/ReportTheta.h
XDE/inst/Test/src/ReportXi.h
XDE/inst/Test/src/Rinterface_v2.cpp
XDE/inst/Test/src/Structure.cpp
XDE/inst/Test/src/Structure.h
XDE/inst/Test/src/Update.h
XDE/inst/Test/src/UpdateAMH.h
XDE/inst/Test/src/UpdateBMH.h
XDE/inst/Test/src/UpdateC2Gibbs.h
XDE/inst/Test/src/UpdateDeltaMH.h
XDE/inst/Test/src/UpdateGamma2Gibbs.h
XDE/inst/Test/src/UpdateLMH.h
XDE/inst/Test/src/UpdateLambdaMH.h
XDE/inst/Test/src/UpdateMultiplicativePositive.h
XDE/inst/Test/src/UpdatePhiMH.h
XDE/inst/Test/src/UpdateRC2MH.h
XDE/inst/Test/src/UpdateRMH.h
XDE/inst/Test/src/UpdateRhoGamma2MH.h
XDE/inst/Test/src/UpdateRhoMH.h
XDE/inst/Test/src/UpdateSigma2MH.h
XDE/inst/Test/src/UpdateTMH.h
XDE/inst/Test/src/UpdateTau2RDDeltaMH.h
XDE/inst/Test/src/UpdateTau2RMH.h
XDE/inst/Test/src/UpdateTau2RhoMH.h
XDE/inst/Test/src/UpdateTau2RhoNuMH.h
XDE/inst/Test/src/UpdateThetaMH.h
XDE/inst/Test/src/UpdateXiGibbs.h
XDE/inst/Test/src/Update_v2.cpp
XDE/inst/Test/src/Update_v2.h
XDE/inst/Test/src/Utility_v2.cpp
XDE/inst/Test/src/Utility_v2.h
XDE/inst/Test/src/diffExpressed_main.cpp
XDE/inst/Test/src/mainTestHyper_v2.cpp
XDE/inst/Test/vignettes
XDE/inst/Test/vignettes/callC.R
XDE/inst/doc
XDE/inst/doc/XDE.R
XDE/inst/doc/XDE.Rnw
XDE/inst/doc/XDE.pdf
XDE/inst/doc/XdeParameterClass.R
XDE/inst/doc/XdeParameterClass.Rnw
XDE/inst/doc/XdeParameterClass.pdf
XDE/inst/logFiles
XDE/inst/logFiles/BES.rda
XDE/inst/logFiles/a.log
XDE/inst/logFiles/b.log
XDE/inst/logFiles/c2.log
XDE/inst/logFiles/gamma2.log
XDE/inst/logFiles/l.log
XDE/inst/logFiles/lambda.log
XDE/inst/logFiles/postAvg.rda
XDE/inst/logFiles/r.log
XDE/inst/logFiles/rho.log
XDE/inst/logFiles/t.log
XDE/inst/logFiles/tau2R.log
XDE/inst/logFiles/tau2Rho.log
XDE/inst/logFiles/theta.log
XDE/inst/logFiles/xi.log
XDE/inst/scripts
XDE/inst/scripts/ModelA_B.R
XDE/inst/scripts/ModelC_D.R
XDE/inst/scripts/ModelI_II.R
XDE/inst/scripts/v2Interface.R
XDE/inst/unitTests
XDE/inst/unitTests/Makefile
XDE/man
XDE/man/ExpressionSetList-class.Rd XDE/man/ExpressionSetList-methods.Rd XDE/man/Parameters-class.Rd XDE/man/XdeMcmc-class.Rd XDE/man/XdeParameter-class.Rd XDE/man/burnin.Rd XDE/man/calculatePosteriorAvg.Rd XDE/man/empiricalStart.Rd XDE/man/expressionSetList.Rd XDE/man/firstMcmc.Rd XDE/man/geneCenter.Rd XDE/man/hyperparameters.Rd XDE/man/iterations.Rd XDE/man/lastMcmc.Rd XDE/man/output.Rd XDE/man/pairs.Rd XDE/man/posteriorAvg.Rd XDE/man/seed.Rd XDE/man/ssStatistic.Rd XDE/man/standardizeSamples.Rd XDE/man/studyCenter.Rd XDE/man/symbolsInteresting.Rd XDE/man/thin.Rd XDE/man/tuning.Rd XDE/man/updates.Rd XDE/man/xde.Rd XDE/man/xmcmc.Rd XDE/man/xsScores.Rd XDE/man/zeroNu.Rd
XDE/src
XDE/src/Cholesky.cpp
XDE/src/Cholesky.h
XDE/src/Makevars
XDE/src/Matrix.h
XDE/src/Matrix_v2.cpp
XDE/src/Matrix_v2.h
XDE/src/Potential.h
XDE/src/PotentialA.h
XDE/src/PotentialB.h
XDE/src/PotentialDDelta.h
XDE/src/PotentialDDeltag.h
XDE/src/PotentialDelta.h
XDE/src/PotentialDeltag.h
XDE/src/PotentialFunction.h
XDE/src/PotentialNu.h
XDE/src/PotentialNug.h
XDE/src/PotentialPhi.h
XDE/src/PotentialPhiqg.h
XDE/src/PotentialR.h
XDE/src/PotentialRho.h
XDE/src/PotentialSigma2.h
XDE/src/PotentialSigma2qg.h
XDE/src/PotentialSum.h
XDE/src/PotentialTau2.h
XDE/src/PotentialX.h
XDE/src/PotentialXi.h
XDE/src/PotentialXqg.h
XDE/src/PotentialZero.h
XDE/src/Potential_v2.cpp
XDE/src/Potential_v2.h
XDE/src/Random.h
XDE/src/Random_v2.cpp
XDE/src/Random_v2.h
XDE/src/Report.h
XDE/src/ReportA.h
XDE/src/ReportAcceptance.h
XDE/src/ReportB.h
XDE/src/ReportC2.h
XDE/src/ReportDDelta.h
XDE/src/ReportDelta.h
XDE/src/ReportDiffexpressed.h
XDE/src/ReportGamma2.h
XDE/src/ReportL.h
XDE/src/ReportLambda.h
XDE/src/ReportNu.h
XDE/src/ReportPhi.h
XDE/src/ReportPotential.h
XDE/src/ReportProbDelta.h
XDE/src/ReportR.h
XDE/src/ReportRho.h
XDE/src/ReportSigma2.h
XDE/src/ReportT.h
XDE/src/ReportTau2R.h
XDE/src/ReportTau2Rho.h
XDE/src/ReportTheta.h
XDE/src/ReportXi.h
XDE/src/Rinterface_v2.cpp
XDE/src/Structure.cpp
XDE/src/Structure.h
XDE/src/Update.h
XDE/src/UpdateAMH.h
XDE/src/UpdateBMH.h
XDE/src/UpdateC2Gibbs.h
XDE/src/UpdateDeltaMH.h
XDE/src/UpdateGamma2Gibbs.h
XDE/src/UpdateLMH.h
XDE/src/UpdateLambdaMH.h
XDE/src/UpdateMultiplicativePositive.h
XDE/src/UpdatePhiMH.h
XDE/src/UpdateRC2MH.h
XDE/src/UpdateRMH.h
XDE/src/UpdateRhoGamma2MH.h
XDE/src/UpdateRhoMH.h
XDE/src/UpdateSigma2MH.h
XDE/src/UpdateTMH.h
XDE/src/UpdateTau2RDDeltaMH.h
XDE/src/UpdateTau2RMH.h
XDE/src/UpdateTau2RhoMH.h
XDE/src/UpdateTau2RhoNuMH.h
XDE/src/UpdateThetaMH.h
XDE/src/UpdateXiGibbs.h
XDE/src/Update_v2.cpp
XDE/src/Update_v2.h
XDE/src/Utility_v2.cpp
XDE/src/Utility_v2.h
XDE/src/diffExpressed_main.cpp
XDE/src/doc
XDE/src/doc/xdeLIN.pdf
XDE/src/doc/xdeLIN.tex
XDE/src/test
XDE/tests
XDE/tests/doRUnit.R
XDE/vignettes
XDE/vignettes/XDE.Rnw
XDE/vignettes/XdeParameterClass.Rnw
XDE/vignettes/genomics.bib

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