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"rowData,SubsetTreeSummarizedExperiment-method", "rowData<-,SubsetRangedSummarizedExperiment-method", "rowData<-,SubsetSingleCellExperiment-method", "rowData<-,SubsetSpatialExperiment-method", "rowData<-,SubsetSummarizedExperiment-method", "rowData<-,SubsetTreeSummarizedExperiment-method" ] }, { "page": "ExperimentSubset-subsetting", "title": "Subset an ExperimentSubset object by rows or columns", "topics": [ "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" ] }, { "page": "getSubsetAssay", "title": "Get subset assay from an 'ExperimentSubset' object.", "topics": [ "getSubsetAssay", "getSubsetAssay,SubsetRangedSummarizedExperiment-method", "getSubsetAssay,SubsetSingleCellExperiment-method", "getSubsetAssay,SubsetSpatialExperiment-method", "getSubsetAssay,SubsetSummarizedExperiment-method", "getSubsetAssay,SubsetTreeSummarizedExperiment-method" ] }, { "page": "getSubsetExperiment", "title": "Take a subset out as a standalone experiment object", "topics": [ "getSubsetExperiment", "getSubsetExperiment,SubsetRangedSummarizedExperiment-method", "getSubsetExperiment,SubsetSingleCellExperiment-method", "getSubsetExperiment,SubsetSpatialExperiment-method", "getSubsetExperiment,SubsetSummarizedExperiment-method", "getSubsetExperiment,SubsetTreeSummarizedExperiment-method" ] }, { "page": "reducedDimNames", "title": "reducedDimNames", "topics": [ "reducedDimNames", "reducedDimNames,ANY-method" ] }, { "page": "reducedDimNames-set", "title": "reducedDimNames<-", "topics": [ "reducedDimNames<-", "reducedDimNames<-,ANY-method" ] }, { "page": "setSubsetAssay", "title": "Method for storing new assays inside subsets in ExperimentSubset objects", "topics": [ "setSubsetAssay", "setSubsetAssay,SubsetRangedSummarizedExperiment-method", "setSubsetAssay,SubsetSingleCellExperiment-method", "setSubsetAssay,SubsetSpatialExperiment-method", "setSubsetAssay,SubsetSummarizedExperiment-method", "setSubsetAssay,SubsetTreeSummarizedExperiment-method" ] }, { "page": "setSubsetExperiment", "title": "Store a standalone experiment object back into a subset", "topics": [ "setSubsetExperiment", "setSubsetExperiment,SubsetRangedSummarizedExperiment-method", "setSubsetExperiment,SubsetSingleCellExperiment-method", "setSubsetExperiment,SubsetSpatialExperiment-method", "setSubsetExperiment,SubsetSummarizedExperiment-method", "setSubsetExperiment,SubsetTreeSummarizedExperiment-method" ] }, { "page": "subsetAssayCount", "title": "Count method for subset assays in ExperimentSubset objects", "topics": [ "subsetAssayCount", "subsetAssayCount,SubsetRangedSummarizedExperiment-method", "subsetAssayCount,SubsetSingleCellExperiment-method", "subsetAssayCount,SubsetSpatialExperiment-method", "subsetAssayCount,SubsetSummarizedExperiment-method", "subsetAssayCount,SubsetTreeSummarizedExperiment-method" ] }, { "page": "subsetAssayNames", "title": "Name retrieval method for all subset assays in ExperimentSubset objects", "topics": [ "subsetAssayNames", "subsetAssayNames,SubsetRangedSummarizedExperiment-method", "subsetAssayNames,SubsetSingleCellExperiment-method", "subsetAssayNames,SubsetSpatialExperiment-method", "subsetAssayNames,SubsetSummarizedExperiment-method", "subsetAssayNames,SubsetTreeSummarizedExperiment-method" ] }, { "page": "subsetColData", "title": "Accessor method for colData from subsets in ExperimentSubset objects", "topics": [ "subsetColData", "subsetColData,SubsetRangedSummarizedExperiment-method", "subsetColData,SubsetSingleCellExperiment-method", "subsetColData,SubsetSpatialExperiment-method", "subsetColData,SubsetSummarizedExperiment-method", "subsetColData,SubsetTreeSummarizedExperiment-method", "subsetColData<-", "subsetColData<-,SubsetRangedSummarizedExperiment-method", 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"subsetColnames<-,SubsetSummarizedExperiment-method", "subsetColnames<-,SubsetTreeSummarizedExperiment-method" ] }, { "page": "subsetColTree", "title": "Get or set the colTree of subsets in ExperimentSubset objects", "topics": [ "subsetColTree", "subsetColTree,SubsetTreeSummarizedExperiment-method", "subsetColTree<-", "subsetColTree<-,SubsetTreeSummarizedExperiment-method" ] }, { "page": "subsetCount", "title": "Subset count method for ExperimentSubset objects", "topics": [ "subsetCount", "subsetCount,SubsetRangedSummarizedExperiment-method", "subsetCount,SubsetSingleCellExperiment-method", "subsetCount,SubsetSpatialExperiment-method", "subsetCount,SubsetSummarizedExperiment-method", "subsetCount,SubsetTreeSummarizedExperiment-method" ] }, { "page": "subsetDim", "title": "Get dimensions of subsets in ExperimentSubset objects", "topics": [ "subsetDim", "subsetDim,SubsetRangedSummarizedExperiment-method", "subsetDim,SubsetSingleCellExperiment-method", "subsetDim,SubsetSpatialExperiment-method", "subsetDim,SubsetSummarizedExperiment-method", "subsetDim,SubsetTreeSummarizedExperiment-method" ] }, { "page": "subsetImgData", "title": "Accessor method for imgData of subsets in ExperimentSubset objects", "topics": [ "subsetImgData", "subsetImgData,SubsetSpatialExperiment-method" ] }, { "page": "subsetNames", "title": "Get names of only the subsets in ExperimentSubset objects", "topics": [ "subsetNames", "subsetNames,SubsetRangedSummarizedExperiment-method", "subsetNames,SubsetSingleCellExperiment-method", "subsetNames,SubsetSpatialExperiment-method", "subsetNames,SubsetSummarizedExperiment-method", "subsetNames,SubsetTreeSummarizedExperiment-method" ] }, { "page": "subsetParent", "title": "Subset parent hierarchy retrieval method for ExperimentSubset objects", "topics": [ "subsetParent", "subsetParent,SubsetRangedSummarizedExperiment-method", "subsetParent,SubsetSingleCellExperiment-method", "subsetParent,SubsetSpatialExperiment-method", "subsetParent,SubsetSummarizedExperiment-method", "subsetParent,SubsetTreeSummarizedExperiment-method" ] }, { "page": "SubsetRangedSummarizedExperiment-class", "title": "An S4 class for 'RangedSummarizedExperiment' objects with added support for subsets.", "topics": [ ".SubsetRangedSummarizedExperiment", "show,SubsetRangedSummarizedExperiment-method", "SubsetRangedSummarizedExperiment-class" ] }, { "page": "subsetRowData", "title": "Accessor method for rowData from subsets in ExperimentSubset objects", "topics": [ "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" ] }, { "page": "subsetRowLinks", "title": "Accessor method for rowLinks from subsets in ExperimentSubset objects", "topics": [ "subsetRowLinks", "subsetRowLinks,SubsetTreeSummarizedExperiment-method" ] }, { "page": "subsetRownames", "title": "subsetRownames", "topics": [ "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" ] }, { "page": "subsetRowTree", "title": "Get or set the rowTree of subsets in ExperimentSubset objects", "topics": [ "subsetRowTree", "subsetRowTree,SubsetTreeSummarizedExperiment-method", "subsetRowTree<-", "subsetRowTree<-,SubsetTreeSummarizedExperiment-method" ] }, { "page": "SubsetSingleCellExperiment-class", "title": "An S4 class for 'SingleCellExperiment' objects with added support for subsets.", "topics": [ ".SubsetSingleCellExperiment", "show,SubsetSingleCellExperiment-method", "SubsetSingleCellExperiment-class" ] }, { "page": "subsetSpatialCoords", "title": "Get or set spatialCoords of subsets in ExperimentSubset objects", "topics": [ "spatialCoords,SubsetSpatialExperiment-method", "subsetSpatialCoords", "subsetSpatialCoords,SubsetSpatialExperiment-method", "subsetSpatialCoords<-", "subsetSpatialCoords<-,SubsetSpatialExperiment-method" ] }, { "page": "subsetSpatialData", "title": "Deprecated: spatialData of subsets in ExperimentSubset objects", "topics": [ "spatialData,SubsetSpatialExperiment-method", 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Campbell", "engine": "knitr::rmarkdown", "headings": [ "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" ], "created": "2020-08-17 09:38:43", "modified": "2026-11-10 14:09:30", "commits": 27 } ], "_score": 5.89209460269048, "_indexed": true, "_nocasepkg": "experimentsubset", "_universes": [ "bioc", "joshua-d-campbell", "campbio" ], "_previous": "1.23.14", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.23.50", "date": "2026-11-11T08:31:03.000Z", "distro": "resolute", "commit": "2c430faee1094f1cfe61b8b3de7cafb730d026d6", "fileid": "https://r2.ropensci.org/f2f0bf4a21757d74cd335d688795e32a68345541f2f4efecb0a8b2d3ae4e0599", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/42986491792" }, { "r": "4.6.2", "os": "linux", "version": "1.23.50", "date": "2026-11-11T08:31:36.000Z", "distro": "resolute", "commit": "2c430faee1094f1cfe61b8b3de7cafb730d026d6", "fileid": "https://r2.ropensci.org/b96732e2f57e1f61e0101f666ba582ed6707b8a92bc4e5d56b9c72bfbd97c52b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/42986491792" }, { "r": "4.5.3", "os": "mac", "version": "1.23.50", "date": "2026-11-11T09:21:04.000Z", "commit": "2c430faee1094f1cfe61b8b3de7cafb730d026d6", "fileid": "https://r2.ropensci.org/fb54c025eb3a6c99af1cf65ede4b0c875b5c427bd98a3eea878743d34d62d6b5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/42986491792" }, { "r": "4.6.2", "os": "mac", "version": "1.23.50", "date": "2026-11-11T09:20:25.000Z", "commit": "2c430faee1094f1cfe61b8b3de7cafb730d026d6", "fileid": "https://r2.ropensci.org/14af6961ef38f3ae1327044a8467e5daab3e8f3a87c2106204700cf87b972d7d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/42986491792" }, { "r": "4.6.0", "os": "wasm", "version": "1.23.50", "date": "2026-11-11T08:30:30.000Z", "commit": "2c430faee1094f1cfe61b8b3de7cafb730d026d6", "fileid": "https://r2.ropensci.org/d05c788f104de988aaf6a32a0886262962cf88ee1c19164cce618ac9435b4b17", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/42986491792" }, { "r": "4.7.0", "os": "win", "version": "1.23.50", "date": "2026-11-11T09:16:16.000Z", "commit": "2c430faee1094f1cfe61b8b3de7cafb730d026d6", "fileid": "https://r2.ropensci.org/3332fe65fa5869742e6bd1eea38d62eedaa0b9692e207f0e85d322c91d9cc5cf", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/42986491792" }, { "r": "4.5.3", "os": "win", "version": "1.23.50", "date": "2026-11-11T09:16:48.000Z", "commit": "2c430faee1094f1cfe61b8b3de7cafb730d026d6", "fileid": "https://r2.ropensci.org/e4ec9c7117c622ed0f484481f1fb17a0473c0c31bb61165e402f0eef845d0d00", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/42986491792" }, { "r": "4.6.2", "os": "win", "version": "1.23.50", "date": "2026-11-11T09:01:19.000Z", "commit": "2c430faee1094f1cfe61b8b3de7cafb730d026d6", "fileid": "https://r2.ropensci.org/3ea65d8bab5ee6b59b71166eaa6f66ea4f6cc1afb7099ffd017ff94e7f076e42", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/42986491792" } ] }