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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("XDE")
AuthorR.B. Scharpf, G. Parmigiani, A.B. Nobel, and H. Tjelmeland
Bioconductor views DifferentialExpression Microarray
Date of publicationNone
MaintainerRobert Scharpf <rscharpf@jhsph.edu>
LicenseLGPL-2
Version2.22.0

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

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

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