Package: XDE 2.53.0
Robert Scharpf
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.
Authors:
XDE_2.53.0.tar.gz
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XDE.pdf |XDE.html✨
XDE/json (API)
NEWS
| # Install 'XDE' in R: |
| install.packages('XDE', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- expressionSetList - Example of ExpressionSetList
- xmcmc - Object of class XdeMcmc
On BioConductor:XDE-2.53.0(bioc 3.21)XDE-2.52.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
microarraydifferentialexpression
Last updated 23 days agofrom:ef93912ae2. Checks:OK: 1 WARNING: 8. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 31 2024 |
| R-4.5-win-x86_64 | WARNING | Oct 31 2024 |
| R-4.5-linux-x86_64 | WARNING | Oct 31 2024 |
| R-4.4-win-x86_64 | WARNING | Oct 31 2024 |
| R-4.4-mac-x86_64 | WARNING | Oct 31 2024 |
| R-4.4-mac-aarch64 | WARNING | Oct 31 2024 |
| R-4.3-win-x86_64 | WARNING | Oct 31 2024 |
| R-4.3-mac-x86_64 | WARNING | Oct 31 2024 |
| R-4.3-mac-aarch64 | WARNING | Oct 31 2024 |
Exports:.standardizedDeltabayesianEffectSizebayesianEffectSize<-burninburnin<-calculateBayesianEffectSizecalculatePosteriorAvgcoercedirectorydirectory<-empiricalStartfeatureDatafeatureNamesfirstMcmcfirstMcmc<-geneCenterhyperparametershyperparameters<-initializeiterationsiterations<-lapplylastMcmclastMcmc<-notesnrownSamplesoutputoutput<-pDataphenotypeLabelphenotypeLabel<-plotposteriorAvgposteriorAvg<-savedIterationsseedseed<-showshowIterationsshowIterations<-ssStatisticstandardizeSamplesstudyCenterstudyNamesstudyNames<-symbolsInterestingthinthin<-tuningtuning<-updatesupdates<-xdexsScoreszeroNu
Dependencies:annotateAnnotationDbiaskpassBiobaseBiocGenericsBiostringsbitbit64blobcachemclicpp11crayoncurlDBIfastmapgenefilterGeneMetagenericsGenomeInfoDbGenomeInfoDbDatagluegtoolshttrIRangesjsonliteKEGGRESTlatticelifecycleMASSMatrixMatrixGenericsmatrixStatsmemoisemimemulttestmvtnormopensslpkgconfigplogrpngR6RColorBrewerrlangRSQLiteS4VectorsscrimesiggenessurvivalsysUCSC.utilsvctrsXMLxtableXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Indicator for running a MCMC burnin | burnin burnin<- |
| Calculate the posterior average for indicators of concordant and discordant differential expression | calculatePosteriorAvg |
| Empirical starting values for the MCMC | empiricalStart |
| Example of ExpressionSetList | expressionSetList |
| A class for containing a list of ExpressionSets | coerce,list,ExpressionSetList-method dim,ExpressionSetList-method ExpressionSetList-class featureNames,ExpressionSetList-method geneCenter,ExpressionSetList-method lapply,ExpressionSetList-method nrow,ExpressionSetList-method nSamples nSamples,ExpressionSetList-method pca,ExpressionSetList-method pData,ExpressionSetList-method phenotype,ExpressionSetList,character-method standardizeSamples,ExpressionSetList-method studyCenter,ExpressionSetList-method zeroNu,ExpressionSetList-method [,ExpressionSetList-method |
| Methods for ExpressionSetList | ExpressionSetList-methods phenotype [,ExpressionSetList,ANY,ANY,ANY-method |
| Values for the first MCMC iteration | firstMcmc firstMcmc<- |
| Center the expression values for each gene in a study to zero | geneCenter |
| Accessor for hyperparameters of the Bayesian model | hyperparameters hyperparameters<- |
| Number of MCMC iterations | iterations iterations<- |
| MCMC values for the last iteration | lastMcmc lastMcmc<- |
| Options for storing results of the MCMC chains | output output<- |
| pairs function for high-throughput data | pairs,data.frame-method pairs,matrix-method pairs-methods |
| Container for XDE parameters | $,Parameters-method $<-,Parameters-method coerce,XdeParameter,Parameters-method Parameters-class show,Parameters-method [[,Parameters-method [[<-,Parameters-method |
| Accessor and replacement methods for posterior averages of differential expression | posteriorAvg posteriorAvg<- |
| Seed for the MCMC | seed seed<- |
| Calculate single study estimates of effect size | ssStatistic |
| Centers the genes at zero and standardizes the samples to have variance 1 | standardizeSamples |
| Center the expression values in a study to zero | studyCenter |
| Useful for changing the look of pairs plots to emphasize concordant or discordant genes | symbolsInteresting |
| How often to write MCMC iterations to file | thin thin<- |
| Tuning parameters for Metropolis-Hastings proposals | tuning tuning<- |
| Frequency of updating a parameter per MCMC iteration | updates updates<- |
| Fit the Bayesian hierarchical model for cross-study differential gene expression | xde |
| Class for storing output from the Bayesian model | $ $,XdeMcmc-method .standardizedDelta,XdeMcmc-method bayesianEffectSize bayesianEffectSize,XdeMcmc-method bayesianEffectSize<- bayesianEffectSize<-,XdeMcmc,matrix-method calculateBayesianEffectSize calculateBayesianEffectSize,XdeMcmc-method calculatePosteriorAvg,XdeMcmc-method directory directory,XdeMcmc-method featureNames,XdeMcmc-method initialize,XdeMcmc-method iterations,XdeMcmc-method lastMcmc,XdeMcmc-method nrow,XdeMcmc-method output,XdeMcmc-method plot,XdeMcmc,ANY-method plot,XdeMcmc-method posteriorAvg,XdeMcmc-method posteriorAvg<-,XdeMcmc,matrix-method seed,XdeMcmc-method show,XdeMcmc-method studyNames,XdeMcmc-method XdeMcmc-class |
| Container class for storing options of the Bayesian hierarchical model | burnin,XdeParameter-method burnin<-,XdeParameter,logical-method coerce,XdeParameter,Params-method directory,XdeParameter-method directory<- directory<-,XdeParameter-method firstMcmc,XdeParameter-method firstMcmc<-,XdeParameter,environment-method firstMcmc<-,XdeParameter,list-method hyperparameters,XdeParameter-method hyperparameters<-,XdeParameter-method initialize,XdeParameter-method iterations,XdeParameter-method iterations<-,XdeParameter,integer-method iterations<-,XdeParameter,numeric-method output,XdeParameter-method output<-,XdeParameter-method phenotypeLabel phenotypeLabel,XdeParameter-method phenotypeLabel<- phenotypeLabel<-,XdeParameter,character-method savedIterations savedIterations,XdeParameter-method seed,XdeParameter-method seed<-,XdeParameter,integer-method seed<-,XdeParameter,numeric-method show,XdeParameter-method showIterations showIterations,XdeParameter-method showIterations<- showIterations<-,XdeParameter-method studyNames studyNames,XdeParameter-method studyNames<- studyNames<-,XdeParameter-method thin,XdeParameter-method thin<-,XdeParameter,numeric-method tuning,XdeParameter-method tuning<-,XdeParameter-method updates,XdeParameter-method updates<-,XdeParameter-method XdeParameter-class |
| Object of class XdeMcmc | xmcmc |
| Alternative cross-study scores of differential expression | xsScores |
| Option for not modeling Nu | zeroNu |