Installation | Motivation | A Brief Description | Overview of the ExperimentSubset class | Core methods of ExperimentSubset class | ExperimentSubset constructor | createSubset | setSubsetAssay and getSubsetAssay | getSubsetExperiment and setSubsetExperiment | subsetSummary | Additional helper methods | subsetColData & subsetRowData | Overridden methods for ExperimentSubset class | assay-get & assay-set inherited methods | Using the ExperimentSubset object: A toy example | Using the ExperimentSubset object: an example with real scRNA-seq data | Supported Input Object Classes | Methods for ExperimentSubset | Implementation Details | Inherited parent object | Additional subsets slot | subsetName | rowIndices | colIndices | parentAssay | internalAssay | Learn more | Session Information
Package: ExperimentSubset 1.23.50
Joshua D. Campbell
ExperimentSubset: Manages Subsets of Data with Bioconductor Experiment Objects
Experiment objects such as the SummarizedExperiment, RangedSummarizedExperiment, SingleCellExperiment, TreeSummarizedExperiment or SpatialExperiment are data containers for one or more matrix-like assays along with the associated row and column data. Often only a subset of the original data is needed for down-stream analysis. For example, filtering out poor quality samples will require excluding some columns before analysis. The ExperimentSubset object is a container to efficiently manage different subsets of the same data without having to make separate objects for each new subset.
Authors:
ExperimentSubset_1.23.50.tar.gz
ExperimentSubset_1.23.50.zip(r-4.7-any)ExperimentSubset_1.23.50.zip(r-4.6-any)ExperimentSubset_1.23.50.zip(r-4.5-any)
ExperimentSubset_1.23.50.tgz(r-4.6-any)ExperimentSubset_1.23.50.tgz(r-4.5-any)
ExperimentSubset_1.23.50.tar.gz(r-4.7-any)ExperimentSubset_1.23.50.tar.gz(r-4.6-any)
ExperimentSubset_1.23.50.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ExperimentSubset/json (API)
| # Install 'ExperimentSubset' in R: |
| install.packages('ExperimentSubset', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/campbio/experimentsubset/issues
On BioConductor:ExperimentSubset-1.23.14(bioc 3.24)ExperimentSubset-1.22.0(bioc 3.23)
infrastructuresoftwaredataimportdatarepresentationsinglecell
Last updated from:2c430faee1. Checks:1 NOTE, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 207 | ||
| linux-devel | OK | 384 | ||
| source / vignettes | OK | 329 | ||
| linux-release | OK | 514 | ||
| macos-release | OK | 429 | ||
| macos-oldrel | OK | 469 | ||
| windows-devel | OK | 3206 | ||
| windows-release | OK | 2257 | ||
| windows-oldrel | OK | 3187 | ||
| wasm-release | OK | 155 |
Exports:createSubsetExperimentSubsetgetSubsetAssaygetSubsetExperimentreducedDimNamesreducedDimNames<-reducedDims<-setSubsetAssaysetSubsetExperimentsubsetAssayCountsubsetAssayNamessubsetColDatasubsetColData<-subsetColLinkssubsetColnamessubsetColnames<-subsetColTreesubsetColTree<-subsetCountsubsetDimsubsetImgDatasubsetNamessubsetParentsubsetRowDatasubsetRowData<-subsetRowLinkssubsetRownamessubsetRownames<-subsetRowTreesubsetRowTree<-subsetSpatialCoordssubsetSpatialCoords<-subsetSpatialDatasubsetSpatialData<-subsetSummary
Dependencies:abindapeaskpassBHBiobaseBiocFileCacheBiocGenericsBiocParallelBiostringsbitbit64blobcachemclicodetoolscpp11crayoncurlDBIdbplyrDelayedArraydigestdplyrfastmapfilelockformatRfsfutile.loggerfutile.optionsgenericsGenomicRangesgluehttr2IRangesjsonlitelambda.rlatticelazyevallifecyclemagickmagrittrMatrixMatrixGenericsmatrixStatsmemoisenlmeopensslpillarpkgconfigpurrrR6rappdirsRcpprjsonrlangRSQLiteS4ArraysS4VectorsSeqinfoSingleCellExperimentsnowSparseArraySpatialExperimentstringistringrSummarizedExperimentsystibbletidyrtidyselecttidytreetreeioTreeSummarizedExperimentutf8vctrswithrXVectoryulab.utils
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Subset creation method for ExperimentSubset objects | createSubset createSubset,SubsetRangedSummarizedExperiment-method createSubset,SubsetSingleCellExperiment-method createSubset,SubsetSpatialExperiment-method createSubset,SubsetSummarizedExperiment-method createSubset,SubsetTreeSummarizedExperiment-method |
| ExperimentSubset constructor | ExperimentSubset |
| Alternative experiments of subsets in ExperimentSubset objects | altExp,SubsetSingleCellExperiment,character-method altExp,SubsetSingleCellExperiment,missing-method altExp,SubsetSingleCellExperiment,numeric-method altExp,SubsetSpatialExperiment,character-method altExp,SubsetSpatialExperiment,missing-method altExp,SubsetSpatialExperiment,numeric-method altExp,SubsetTreeSummarizedExperiment,character-method altExp,SubsetTreeSummarizedExperiment,missing-method altExp,SubsetTreeSummarizedExperiment,numeric-method altExp<-,SubsetSingleCellExperiment,character-method altExp<-,SubsetSingleCellExperiment,missing-method altExp<-,SubsetSingleCellExperiment,numeric-method altExp<-,SubsetSpatialExperiment,character-method altExp<-,SubsetSpatialExperiment,missing-method altExp<-,SubsetSpatialExperiment,numeric-method altExp<-,SubsetTreeSummarizedExperiment,character-method altExp<-,SubsetTreeSummarizedExperiment,missing-method altExp<-,SubsetTreeSummarizedExperiment,numeric-method altExpNames,SubsetSingleCellExperiment-method altExpNames,SubsetSpatialExperiment-method altExpNames,SubsetTreeSummarizedExperiment-method altExpNames<-,SubsetSingleCellExperiment,ANY-method altExpNames<-,SubsetSingleCellExperiment,character-method altExpNames<-,SubsetSpatialExperiment,ANY-method altExpNames<-,SubsetSpatialExperiment,character-method altExpNames<-,SubsetTreeSummarizedExperiment,ANY-method altExpNames<-,SubsetTreeSummarizedExperiment,character-method altExps,SubsetSingleCellExperiment-method altExps,SubsetSpatialExperiment-method altExps,SubsetTreeSummarizedExperiment-method altExps<-,SubsetSingleCellExperiment-method altExps<-,SubsetSpatialExperiment-method altExps<-,SubsetTreeSummarizedExperiment-method ExperimentSubset-altExp |
| Assays of subsets in ExperimentSubset objects | assay,SubsetRangedSummarizedExperiment,character-method assay,SubsetSingleCellExperiment,character-method assay,SubsetSpatialExperiment,character-method assay,SubsetSummarizedExperiment,character-method assay,SubsetTreeSummarizedExperiment,character-method assay<-,SubsetRangedSummarizedExperiment,character-method assay<-,SubsetSingleCellExperiment,character-method assay<-,SubsetSpatialExperiment,character-method assay<-,SubsetSummarizedExperiment,character-method assay<-,SubsetTreeSummarizedExperiment,character-method ExperimentSubset-assay |
| The class of every ExperimentSubset object | ExperimentSubset-class |
| Combine ExperimentSubset objects by columns or rows | cbind,SubsetRangedSummarizedExperiment-method cbind,SubsetSingleCellExperiment-method cbind,SubsetSpatialExperiment-method cbind,SubsetSummarizedExperiment-method cbind,SubsetTreeSummarizedExperiment-method combineCols,SubsetRangedSummarizedExperiment-method combineCols,SubsetSingleCellExperiment-method combineCols,SubsetSpatialExperiment-method combineCols,SubsetSummarizedExperiment-method combineCols,SubsetTreeSummarizedExperiment-method combineRows,SubsetRangedSummarizedExperiment-method combineRows,SubsetSingleCellExperiment-method combineRows,SubsetSpatialExperiment-method combineRows,SubsetSummarizedExperiment-method combineRows,SubsetTreeSummarizedExperiment-method ExperimentSubset-combine rbind,SubsetRangedSummarizedExperiment-method rbind,SubsetSingleCellExperiment-method rbind,SubsetSpatialExperiment-method rbind,SubsetSummarizedExperiment-method rbind,SubsetTreeSummarizedExperiment-method |
| Metadata of subsets in ExperimentSubset objects | ExperimentSubset-metadata metadata,SubsetRangedSummarizedExperiment-method metadata,SubsetSingleCellExperiment-method metadata,SubsetSpatialExperiment-method metadata,SubsetSummarizedExperiment-method metadata,SubsetTreeSummarizedExperiment-method metadata<-,SubsetRangedSummarizedExperiment-method metadata<-,SubsetSingleCellExperiment-method metadata<-,SubsetSpatialExperiment-method metadata<-,SubsetSummarizedExperiment-method metadata<-,SubsetTreeSummarizedExperiment-method |
| Reduced dimensions of subsets in ExperimentSubset objects | ExperimentSubset-reducedDim reducedDim,SubsetSingleCellExperiment,character-method reducedDim,SubsetSingleCellExperiment,missing-method reducedDim,SubsetSingleCellExperiment,numeric-method reducedDim,SubsetSpatialExperiment,character-method reducedDim,SubsetSpatialExperiment,missing-method reducedDim,SubsetSpatialExperiment,numeric-method reducedDim,SubsetTreeSummarizedExperiment,character-method reducedDim,SubsetTreeSummarizedExperiment,missing-method reducedDim,SubsetTreeSummarizedExperiment,numeric-method reducedDim<-,SubsetSingleCellExperiment,character-method reducedDim<-,SubsetSingleCellExperiment,missing-method reducedDim<-,SubsetSingleCellExperiment,numeric-method reducedDim<-,SubsetSpatialExperiment,character-method reducedDim<-,SubsetSpatialExperiment,missing-method reducedDim<-,SubsetSpatialExperiment,numeric-method reducedDim<-,SubsetTreeSummarizedExperiment,character-method reducedDim<-,SubsetTreeSummarizedExperiment,missing-method reducedDim<-,SubsetTreeSummarizedExperiment,numeric-method reducedDims,SubsetSingleCellExperiment-method reducedDims,SubsetSpatialExperiment-method reducedDims,SubsetTreeSummarizedExperiment-method reducedDims<-,SubsetSingleCellExperiment-method reducedDims<-,SubsetSpatialExperiment-method reducedDims<-,SubsetTreeSummarizedExperiment-method |
| rowData and colData of subsets in ExperimentSubset objects | colData,SubsetRangedSummarizedExperiment-method colData,SubsetSingleCellExperiment-method colData,SubsetSpatialExperiment-method colData,SubsetSummarizedExperiment-method colData,SubsetTreeSummarizedExperiment-method colData<-,SubsetRangedSummarizedExperiment,ANY-method colData<-,SubsetRangedSummarizedExperiment,data.frame-method colData<-,SubsetRangedSummarizedExperiment,DataFrame-method colData<-,SubsetRangedSummarizedExperiment,NULL-method colData<-,SubsetSingleCellExperiment,ANY-method colData<-,SubsetSingleCellExperiment,data.frame-method colData<-,SubsetSingleCellExperiment,DataFrame-method colData<-,SubsetSingleCellExperiment,NULL-method colData<-,SubsetSpatialExperiment,ANY-method colData<-,SubsetSpatialExperiment,data.frame-method colData<-,SubsetSpatialExperiment,DataFrame-method colData<-,SubsetSpatialExperiment,NULL-method colData<-,SubsetSummarizedExperiment,ANY-method colData<-,SubsetSummarizedExperiment,data.frame-method colData<-,SubsetSummarizedExperiment,DataFrame-method colData<-,SubsetSummarizedExperiment,NULL-method colData<-,SubsetTreeSummarizedExperiment,ANY-method colData<-,SubsetTreeSummarizedExperiment,data.frame-method colData<-,SubsetTreeSummarizedExperiment,DataFrame-method colData<-,SubsetTreeSummarizedExperiment,NULL-method ExperimentSubset-rowData-colData rowData,SubsetRangedSummarizedExperiment-method rowData,SubsetSingleCellExperiment-method rowData,SubsetSpatialExperiment-method rowData,SubsetSummarizedExperiment-method rowData,SubsetTreeSummarizedExperiment-method rowData<-,SubsetRangedSummarizedExperiment-method rowData<-,SubsetSingleCellExperiment-method rowData<-,SubsetSpatialExperiment-method rowData<-,SubsetSummarizedExperiment-method rowData<-,SubsetTreeSummarizedExperiment-method |
| Subset an ExperimentSubset object by rows or columns | ExperimentSubset-subsetting [,SubsetRangedSummarizedExperiment,ANY,ANY,ANY-method [,SubsetSingleCellExperiment,ANY,ANY,ANY-method [,SubsetSpatialExperiment,ANY,ANY,ANY-method [,SubsetSummarizedExperiment,ANY,ANY,ANY-method [,SubsetTreeSummarizedExperiment,ANY,ANY,ANY-method |
| Get subset assay from an 'ExperimentSubset' object. | getSubsetAssay getSubsetAssay,SubsetRangedSummarizedExperiment-method getSubsetAssay,SubsetSingleCellExperiment-method getSubsetAssay,SubsetSpatialExperiment-method getSubsetAssay,SubsetSummarizedExperiment-method getSubsetAssay,SubsetTreeSummarizedExperiment-method |
| Take a subset out as a standalone experiment object | getSubsetExperiment getSubsetExperiment,SubsetRangedSummarizedExperiment-method getSubsetExperiment,SubsetSingleCellExperiment-method getSubsetExperiment,SubsetSpatialExperiment-method getSubsetExperiment,SubsetSummarizedExperiment-method getSubsetExperiment,SubsetTreeSummarizedExperiment-method |
| reducedDimNames | reducedDimNames reducedDimNames,ANY-method |
| reducedDimNames<- | reducedDimNames<- reducedDimNames<-,ANY-method |
| Method for storing new assays inside subsets in ExperimentSubset objects | setSubsetAssay setSubsetAssay,SubsetRangedSummarizedExperiment-method setSubsetAssay,SubsetSingleCellExperiment-method setSubsetAssay,SubsetSpatialExperiment-method setSubsetAssay,SubsetSummarizedExperiment-method setSubsetAssay,SubsetTreeSummarizedExperiment-method |
| Store a standalone experiment object back into a subset | setSubsetExperiment setSubsetExperiment,SubsetRangedSummarizedExperiment-method setSubsetExperiment,SubsetSingleCellExperiment-method setSubsetExperiment,SubsetSpatialExperiment-method setSubsetExperiment,SubsetSummarizedExperiment-method setSubsetExperiment,SubsetTreeSummarizedExperiment-method |
| Count method for subset assays in ExperimentSubset objects | subsetAssayCount subsetAssayCount,SubsetRangedSummarizedExperiment-method subsetAssayCount,SubsetSingleCellExperiment-method subsetAssayCount,SubsetSpatialExperiment-method subsetAssayCount,SubsetSummarizedExperiment-method subsetAssayCount,SubsetTreeSummarizedExperiment-method |
| Name retrieval method for all subset assays in ExperimentSubset objects | subsetAssayNames subsetAssayNames,SubsetRangedSummarizedExperiment-method subsetAssayNames,SubsetSingleCellExperiment-method subsetAssayNames,SubsetSpatialExperiment-method subsetAssayNames,SubsetSummarizedExperiment-method subsetAssayNames,SubsetTreeSummarizedExperiment-method |
| Accessor method for colData from subsets in ExperimentSubset objects | subsetColData subsetColData,SubsetRangedSummarizedExperiment-method subsetColData,SubsetSingleCellExperiment-method subsetColData,SubsetSpatialExperiment-method subsetColData,SubsetSummarizedExperiment-method subsetColData,SubsetTreeSummarizedExperiment-method subsetColData<- subsetColData<-,SubsetRangedSummarizedExperiment-method subsetColData<-,SubsetSingleCellExperiment-method subsetColData<-,SubsetSpatialExperiment-method subsetColData<-,SubsetSummarizedExperiment-method subsetColData<-,SubsetTreeSummarizedExperiment-method |
| Accessor method for colLinks from subsets in ExperimentSubset objects | subsetColLinks subsetColLinks,SubsetTreeSummarizedExperiment-method |
| subsetColnames | subsetColnames subsetColnames,SubsetRangedSummarizedExperiment-method subsetColnames,SubsetSingleCellExperiment-method subsetColnames,SubsetSpatialExperiment-method subsetColnames,SubsetSummarizedExperiment-method subsetColnames,SubsetTreeSummarizedExperiment-method subsetColnames<- subsetColnames<-,SubsetRangedSummarizedExperiment-method subsetColnames<-,SubsetSingleCellExperiment-method subsetColnames<-,SubsetSpatialExperiment-method subsetColnames<-,SubsetSummarizedExperiment-method subsetColnames<-,SubsetTreeSummarizedExperiment-method |
| Get or set the colTree of subsets in ExperimentSubset objects | subsetColTree subsetColTree,SubsetTreeSummarizedExperiment-method subsetColTree<- subsetColTree<-,SubsetTreeSummarizedExperiment-method |
| Subset count method for ExperimentSubset objects | subsetCount subsetCount,SubsetRangedSummarizedExperiment-method subsetCount,SubsetSingleCellExperiment-method subsetCount,SubsetSpatialExperiment-method subsetCount,SubsetSummarizedExperiment-method subsetCount,SubsetTreeSummarizedExperiment-method |
| Get dimensions of subsets in ExperimentSubset objects | subsetDim subsetDim,SubsetRangedSummarizedExperiment-method subsetDim,SubsetSingleCellExperiment-method subsetDim,SubsetSpatialExperiment-method subsetDim,SubsetSummarizedExperiment-method subsetDim,SubsetTreeSummarizedExperiment-method |
| Accessor method for imgData of subsets in ExperimentSubset objects | subsetImgData subsetImgData,SubsetSpatialExperiment-method |
| Get names of only the subsets in ExperimentSubset objects | subsetNames subsetNames,SubsetRangedSummarizedExperiment-method subsetNames,SubsetSingleCellExperiment-method subsetNames,SubsetSpatialExperiment-method subsetNames,SubsetSummarizedExperiment-method subsetNames,SubsetTreeSummarizedExperiment-method |
| Subset parent hierarchy retrieval method for ExperimentSubset objects | subsetParent subsetParent,SubsetRangedSummarizedExperiment-method subsetParent,SubsetSingleCellExperiment-method subsetParent,SubsetSpatialExperiment-method subsetParent,SubsetSummarizedExperiment-method subsetParent,SubsetTreeSummarizedExperiment-method |
| An S4 class for 'RangedSummarizedExperiment' objects with added support for subsets. | .SubsetRangedSummarizedExperiment show,SubsetRangedSummarizedExperiment-method SubsetRangedSummarizedExperiment-class |
| Accessor method for rowData from subsets in ExperimentSubset objects | subsetRowData subsetRowData,SubsetRangedSummarizedExperiment-method subsetRowData,SubsetSingleCellExperiment-method subsetRowData,SubsetSpatialExperiment-method subsetRowData,SubsetSummarizedExperiment-method subsetRowData,SubsetTreeSummarizedExperiment-method subsetRowData<- subsetRowData<-,SubsetRangedSummarizedExperiment-method subsetRowData<-,SubsetSingleCellExperiment-method subsetRowData<-,SubsetSpatialExperiment-method subsetRowData<-,SubsetSummarizedExperiment-method subsetRowData<-,SubsetTreeSummarizedExperiment-method |
| Accessor method for rowLinks from subsets in ExperimentSubset objects | subsetRowLinks subsetRowLinks,SubsetTreeSummarizedExperiment-method |
| subsetRownames | subsetRownames subsetRownames,SubsetRangedSummarizedExperiment-method subsetRownames,SubsetSingleCellExperiment-method subsetRownames,SubsetSpatialExperiment-method subsetRownames,SubsetSummarizedExperiment-method subsetRownames,SubsetTreeSummarizedExperiment-method subsetRownames<- subsetRownames<-,SubsetRangedSummarizedExperiment-method subsetRownames<-,SubsetSingleCellExperiment-method subsetRownames<-,SubsetSpatialExperiment-method subsetRownames<-,SubsetSummarizedExperiment-method subsetRownames<-,SubsetTreeSummarizedExperiment-method |
| Get or set the rowTree of subsets in ExperimentSubset objects | subsetRowTree subsetRowTree,SubsetTreeSummarizedExperiment-method subsetRowTree<- subsetRowTree<-,SubsetTreeSummarizedExperiment-method |
| An S4 class for 'SingleCellExperiment' objects with added support for subsets. | .SubsetSingleCellExperiment show,SubsetSingleCellExperiment-method SubsetSingleCellExperiment-class |
| Get or set spatialCoords of subsets in ExperimentSubset objects | spatialCoords,SubsetSpatialExperiment-method subsetSpatialCoords subsetSpatialCoords,SubsetSpatialExperiment-method subsetSpatialCoords<- subsetSpatialCoords<-,SubsetSpatialExperiment-method |
| Deprecated: spatialData of subsets in ExperimentSubset objects | spatialData,SubsetSpatialExperiment-method subsetSpatialData subsetSpatialData,SubsetSpatialExperiment-method subsetSpatialData<- subsetSpatialData<-,SubsetSpatialExperiment-method |
| An S4 class for 'SpatialExperiment' objects with added support for subsets. | .SubsetSpatialExperiment show,SubsetSpatialExperiment-method SubsetSpatialExperiment-class |
| An S4 class for 'SummarizedExperiment' objects with added support for subsets. | .SubsetSummarizedExperiment show,SubsetSummarizedExperiment-method SubsetSummarizedExperiment-class |
| Method for displaying 'child-parent' link structure of subsets in ExperimentSubset objects | subsetSummary subsetSummary,SubsetRangedSummarizedExperiment-method subsetSummary,SubsetSingleCellExperiment-method subsetSummary,SubsetSpatialExperiment-method subsetSummary,SubsetSummarizedExperiment-method subsetSummary,SubsetTreeSummarizedExperiment-method |
| An S4 class for 'TreeSummarizedExperiment' objects with added support for subsets. | .SubsetTreeSummarizedExperiment show,SubsetTreeSummarizedExperiment-method SubsetTreeSummarizedExperiment-class |