Installation | Introduction | Relationship to existing Bioconductor packages | Introducing ReducedExperiment containers with a case study | The case study data | Applying factor analysis | Module analysis | Identifying factor and module associations | Finding functional enrichments for factors and modules | Applying factors and modules to new datasets | Factor projection | Applying modules to new data | Module preservation | Extending the ReducedExperiment class | Constructing a ReducedExperiment from scratch | Vignette references | Session Information
Package: ReducedExperiment 1.5.0
Jack Gisby
ReducedExperiment: Containers and tools for dimensionally-reduced -omics representations
Provides SummarizedExperiment-like containers for storing and manipulating dimensionally-reduced assay data. The ReducedExperiment classes allow users to simultaneously manipulate their original dataset and their decomposed data, in addition to other method-specific outputs like feature loadings. Implements utilities and specialised classes for the application of stabilised independent component analysis (sICA) and weighted gene correlation network analysis (WGCNA).
Authors:
ReducedExperiment_1.5.0.tar.gz
ReducedExperiment_1.5.0.zip(r-4.7)ReducedExperiment_1.5.0.zip(r-4.6)ReducedExperiment_1.5.0.zip(r-4.5)
ReducedExperiment_1.5.0.tgz(r-4.6-any)ReducedExperiment_1.5.0.tgz(r-4.5-any)
ReducedExperiment_1.5.0.tar.gz(r-4.7-any)ReducedExperiment_1.5.0.tar.gz(r-4.6-any)
ReducedExperiment_1.5.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ReducedExperiment/json (API)
| # Install 'ReducedExperiment' in R: |
| install.packages('ReducedExperiment', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/jackgisby/reducedexperiment/issues
On BioConductor:ReducedExperiment-1.5.0(bioc 3.24)ReducedExperiment-1.4.0(bioc 3.23)
geneexpressioninfrastructuredatarepresentationsoftwaredimensionreductionnetworkbioconductor-packagebioinformaticsdimensionality-reduction
Last updated from:a184d2159b. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 279 | ||
| linux-devel-x86_64 | NOTE | 651 | ||
| source / vignettes | OK | 459 | ||
| linux-release-x86_64 | NOTE | 655 | ||
| macos-release-arm64 | NOTE | 431 | ||
| macos-oldrel-arm64 | NOTE | 488 | ||
| windows-devel | NOTE | 487 | ||
| windows-release | NOTE | 450 | ||
| windows-oldrel | NOTE | 470 | ||
| wasm-release | OK | 245 |
Exports:assessSoftThresholdassignmentsassignments<-associateComponentscalcEigengenescbindcolnames<-componentNamescomponentNames<-dendrogramdendrogram<-estimateFactorsestimateStabilityFactorisedExperimentfeatureNamesfeatureNames<-getAlignedFeaturesgetCentralitygetCommonFeaturesgetGeneIDsgetMsigdbT2GidentifyModulesloadingsloadings<-ModularExperimentmoduleNamesmoduleNames<-modulePreservationnComponentsnFeaturesnModulesnSamplesplotCommonFeaturesplotDendroplotModulePreservationplotStabilitypredictprojectDatarbindreducedreduced<-ReducedExperimentrownames<-ROWNAMES<-runEnrichrunICArunWGCNAsampleNamessampleNames<-showstabilitystability<-
Dependencies:abindaisdkAnnotationDbiapeaplotaskpassassertthatbabelgenebackportsbase64encBHBiobaseBiocFileCacheBiocGenericsBiocParallelbiomaRtBiostringsbitbit64blobbootbroombslibcachemcallrcarcarDatacheckmatecliclusterclusterProfilercodetoolscolorspacecowplotcpp11crayoncurldata.tableDBIdbplyrDelayedArrayDerivdigestdoBydoParallelDOSEdplyrdynamicTreeCutenrichitenrichplotevaluatefarverfastclusterfastmapfilelockfontawesomefontBitstreamVerafontLiberationfontquiverforeachforecastforeignformatRFormulafracdifffsfutile.loggerfutile.optionsgdtoolsgenericsGenomicRangesggforceggfunggiraphggnewscaleggplot2ggplotifyggrepelggtangleggtreeglueGO.dbGOSemSimgridExtragridGraphicsgsongtablehighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2icaigraphimputeIRangesisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelazyevallifecyclelme4lmerTestlmtestmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmimeminqamodelrmomentsmsigdbrnlmenloptrnnetnumDerivopensslotelpatchworkpbkrtestpheatmappillarpkgconfigplyrpngpolyclippreprocessCoreprettyunitsprocessxprogresspspurrrquantregqvalueR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasreshape2rlangrmarkdownrpartRSQLiterstudioapiS4ArraysS4VectorsS7sassscalesscatterpieSeqinfosnowSparseArraySparseMstringistringrSummarizedExperimentsurvivalsyssystemfontstibbletidydrtidyrtidyselecttidytreetimeDatetinytextreeiotweenrurcautf8vctrsviridisLiteWGCNAwithrxfunxml2XVectoryamlyulab.utilszoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Command line completion for '$' | .DollarNames.FactorisedExperiment .DollarNames.ModularExperiment .DollarNames.ReducedExperiment dollar_names |
| Extract and replace parts of ReducedExperiment objects | slice [,FactorisedExperiment,ANY,ANY,ANY-method [,ModularExperiment,ANY,ANY,ANY-method [,ReducedExperiment,ANY,ANY,ANY-method [<-,FactorisedExperiment,ANY,ANY,FactorisedExperiment-method [<-,ModularExperiment,ANY,ANY,ModularExperiment-method [<-,ReducedExperiment,ANY,ANY,ReducedExperiment-method |
| Assess soft thresholding power for WGCNA | assessSoftThreshold |
| Get and set module feature assignments | assignments assignments,ModularExperiment-method assignments<- assignments<-,ModularExperiment-method |
| Runs linear models for components and sample-level data | associateComponents |
| Calculate eigengenes for new data | calcEigengenes calcEigengenes,ModularExperiment,data.frame-method calcEigengenes,ModularExperiment,matrix-method calcEigengenes,ModularExperiment,SummarizedExperiment-method predict,ModularExperiment-method |
| Combine ReducedExperiment objects by columns or rows | cbind,FactorisedExperiment-method cbind,ModularExperiment-method cbind,ReducedExperiment-method cbind_rbind rbind,FactorisedExperiment-method rbind,ModularExperiment-method rbind,ReducedExperiment-method |
| Get names of dimensionally-reduced components | componentNames componentNames,ReducedExperiment-method componentNames<- componentNames<-,FactorisedExperiment-method componentNames<-,ModularExperiment-method componentNames<-,ReducedExperiment-method moduleNames moduleNames,ModularExperiment-method moduleNames<- moduleNames<-,ModularExperiment-method |
| Get the dendrogram stored in a ModularExperiment | dendrogram dendrogram,ModularExperiment-method dendrogram<- dendrogram<-,ModularExperiment-method |
| Get the dimensions of a Reducedexperiment object | dim,ReducedExperiment-method |
| Perform dimensionality reduction using Independent Component Analysis | estimateFactors |
| Estimate stability of factors as a function of the number of components | estimateStability |
| FactorisedExperiment: A container for the results of factor analysis | .FactorisedExperiment FactorisedExperiment FactorisedExperiment-class |
| Get feature alignments with factors | getAlignedFeatures getAlignedFeatures,FactorisedExperiment-method |
| Get correlation of features with module eigengenes | getCentrality getCentrality,ModularExperiment-method |
| Get common factor features | getCommonFeatures |
| Gets alternative gene annotations from biomaRt | getGeneIDs getGeneIDs,ReducedExperiment-method |
| Get TERM2GENE dataframe from MSigDB | getMsigdbT2G |
| Apply dimensionality reduction using Weighted Gene Correlation Network Analysis | identifyModules |
| Get and set loadings | loadings loadings,FactorisedExperiment-method loadings,ModularExperiment-method loadings<- loadings<-,FactorisedExperiment-method loadings<-,ModularExperiment-method |
| ModularExperiment: A container for the results of module analysis | .ModularExperiment ModularExperiment ModularExperiment-class |
| Get module preservation statistics | modulePreservation |
| Get feature names | featureNames featureNames,ReducedExperiment-method featureNames<- featureNames<-,FactorisedExperiment-method featureNames<-,ModularExperiment-method featureNames<-,ReducedExperiment-method names<-,FactorisedExperiment-method names<-,ModularExperiment-method names<-,ReducedExperiment-method rownames<-,FactorisedExperiment-method rownames<-,ModularExperiment-method ROWNAMES<-,ReducedExperiment-method rownames<-,ReducedExperiment-method |
| Prints individual lengths of samples, components and features | individual_dim nComponents nComponents,ReducedExperiment-method nFeatures nFeatures,ReducedExperiment-method nModules nModules,ModularExperiment-method nSamples nSamples,ReducedExperiment-method |
| Heatmap comparing commonality across factors | plotCommonFeatures |
| Plot a dendrogram stored in a ModularExperiment | plotDendro plotDendro,ModularExperiment-method |
| Plot module preservation statistics | plotModulePreservation |
| Plot component stability as a function of the number of components | plotStability |
| Project new data using pre-defined factors | predict,FactorisedExperiment-method projectData projectData,FactorisedExperiment,data.frame-method projectData,FactorisedExperiment,matrix-method projectData,FactorisedExperiment,SummarizedExperiment-method |
| Get and set reduced data | reduced reduced,ReducedExperiment-method reduced<- reduced<-,ReducedExperiment-method |
| ReducedExperiment: A container for dimensionally-reduced representations | .ReducedExperiment ReducedExperiment ReducedExperiment-class |
| Functional enrichment analyses for dimensionally-reduced data | runEnrich runEnrich,FactorisedExperiment-method runEnrich,ModularExperiment-method |
| Run standard or stabilised Independent Component Analysis | runICA |
| Run WGCNA for a data matrix | runWGCNA |
| Get sample names | colnames<-,ReducedExperiment-method sampleNames sampleNames,ReducedExperiment-method sampleNames<- sampleNames<-,ReducedExperiment-method |
| Prints a summary of a ReducedExperiment object | show show,ReducedExperiment-method |
| Get and setting the stability values for factors | stability stability,FactorisedExperiment-method stability<- stability<-,FactorisedExperiment-method |
