Package index • ExperimentSubset

Constructor and classes

ExperimentSubset(): ExperimentSubset constructor
ExperimentSubset-class: The class of every ExperimentSubset object
show(<SubsetRangedSummarizedExperiment>): An S4 class for RangedSummarizedExperiment objects with added support for subsets.
show(<SubsetSingleCellExperiment>): An S4 class for SingleCellExperiment objects with added support for subsets.
show(<SubsetSpatialExperiment>): An S4 class for SpatialExperiment objects with added support for subsets.
show(<SubsetSummarizedExperiment>): An S4 class for SummarizedExperiment objects with added support for subsets.
show(<SubsetTreeSummarizedExperiment>): An S4 class for TreeSummarizedExperiment objects with added support for subsets.

Creating and managing subsets

createSubset(): Subset creation method for ExperimentSubset objects
subsetNames(): Get names of only the subsets in ExperimentSubset objects
subsetCount(): Subset count method for ExperimentSubset objects
subsetDim(): Get dimensions of subsets in ExperimentSubset objects
subsetParent(): Subset parent hierarchy retrieval method for ExperimentSubset objects
subsetSummary(): Method for displaying 'child-parent' link structure of subsets in ExperimentSubset objects
subsetAssayNames(): Name retrieval method for all subset assays in ExperimentSubset objects
subsetAssayCount(): Count method for subset assays in ExperimentSubset objects
`[`(<SubsetRangedSummarizedExperiment>,<ANY>,<ANY>,<ANY>) `[`(<SubsetSingleCellExperiment>,<ANY>,<ANY>,<ANY>) `[`(<SubsetSummarizedExperiment>,<ANY>,<ANY>,<ANY>) `[`(<SubsetSpatialExperiment>,<ANY>,<ANY>,<ANY>) `[`(<SubsetTreeSummarizedExperiment>,<ANY>,<ANY>,<ANY>): Subset an ExperimentSubset object by rows or columns
cbind(<SubsetRangedSummarizedExperiment>) rbind(<SubsetRangedSummarizedExperiment>) combineCols(<SubsetRangedSummarizedExperiment>) combineRows(<SubsetRangedSummarizedExperiment>) cbind(<SubsetSingleCellExperiment>) rbind(<SubsetSingleCellExperiment>) combineCols(<SubsetSingleCellExperiment>) combineRows(<SubsetSingleCellExperiment>) cbind(<SubsetSummarizedExperiment>) rbind(<SubsetSummarizedExperiment>) combineCols(<SubsetSummarizedExperiment>) combineRows(<SubsetSummarizedExperiment>) cbind(<SubsetSpatialExperiment>) rbind(<SubsetSpatialExperiment>) combineCols(<SubsetSpatialExperiment>) combineRows(<SubsetSpatialExperiment>) cbind(<SubsetTreeSummarizedExperiment>) rbind(<SubsetTreeSummarizedExperiment>) combineCols(<SubsetTreeSummarizedExperiment>) combineRows(<SubsetTreeSummarizedExperiment>): Combine ExperimentSubset objects by columns or rows

Getting and setting subset data

getSubsetAssay(): Get subset assay from an ExperimentSubset object.
setSubsetAssay(): Method for storing new assays inside subsets in ExperimentSubset objects
getSubsetExperiment(): Take a subset out as a standalone experiment object
setSubsetExperiment(): Store a standalone experiment object back into a subset
subsetRowData() `subsetRowData<-`(): Accessor method for rowData from subsets in ExperimentSubset objects
subsetColData() `subsetColData<-`(): Accessor method for colData from subsets in ExperimentSubset objects
subsetRownames() `subsetRownames<-`(): subsetRownames
subsetColnames() `subsetColnames<-`(): subsetColnames

Class-specific accessors

Tree links of a TreeSummarizedExperiment and spatial data of a SpatialExperiment, for a subset.

subsetRowLinks(): Accessor method for rowLinks from subsets in ExperimentSubset objects
subsetColLinks(): Accessor method for colLinks from subsets in ExperimentSubset objects
subsetRowTree() `subsetRowTree<-`(): Get or set the rowTree of subsets in ExperimentSubset objects
subsetColTree() `subsetColTree<-`(): Get or set the colTree of subsets in ExperimentSubset objects
subsetSpatialCoords() `subsetSpatialCoords<-`() spatialCoords(<SubsetSpatialExperiment>): Get or set spatialCoords of subsets in ExperimentSubset objects
subsetImgData(): Accessor method for imgData of subsets in ExperimentSubset objects
subsetSpatialData() `subsetSpatialData<-`() spatialData(<SubsetSpatialExperiment>): Deprecated: spatialData of subsets in ExperimentSubset objects

Methods that take subsetName

Methods of Bioconductor generics that read or set a subset’s data when given subsetName, and otherwise act on the main object. assay() and assay<- name the subset with i instead.

assay(<SubsetRangedSummarizedExperiment>,<character>) `assay<-`(<SubsetRangedSummarizedExperiment>,<character>) assay(<SubsetSingleCellExperiment>,<character>) `assay<-`(<SubsetSingleCellExperiment>,<character>) assay(<SubsetSummarizedExperiment>,<character>) `assay<-`(<SubsetSummarizedExperiment>,<character>) assay(<SubsetSpatialExperiment>,<character>) `assay<-`(<SubsetSpatialExperiment>,<character>) assay(<SubsetTreeSummarizedExperiment>,<character>) `assay<-`(<SubsetTreeSummarizedExperiment>,<character>): Assays of subsets in ExperimentSubset objects
rowData(<SubsetRangedSummarizedExperiment>) colData(<SubsetRangedSummarizedExperiment>) `rowData<-`(<SubsetRangedSummarizedExperiment>) `colData<-`(<SubsetRangedSummarizedExperiment>,<DataFrame>) `colData<-`(<SubsetRangedSummarizedExperiment>,<NULL>) `colData<-`(<SubsetRangedSummarizedExperiment>,<data.frame>) `colData<-`(<SubsetRangedSummarizedExperiment>,<ANY>) rowData(<SubsetSingleCellExperiment>) colData(<SubsetSingleCellExperiment>) `rowData<-`(<SubsetSingleCellExperiment>) `colData<-`(<SubsetSingleCellExperiment>,<DataFrame>) `colData<-`(<SubsetSingleCellExperiment>,<NULL>) `colData<-`(<SubsetSingleCellExperiment>,<data.frame>) `colData<-`(<SubsetSingleCellExperiment>,<ANY>) rowData(<SubsetSummarizedExperiment>) colData(<SubsetSummarizedExperiment>) `rowData<-`(<SubsetSummarizedExperiment>) `colData<-`(<SubsetSummarizedExperiment>,<DataFrame>) `colData<-`(<SubsetSummarizedExperiment>,<NULL>) `colData<-`(<SubsetSummarizedExperiment>,<data.frame>) `colData<-`(<SubsetSummarizedExperiment>,<ANY>) rowData(<SubsetSpatialExperiment>) colData(<SubsetSpatialExperiment>) `rowData<-`(<SubsetSpatialExperiment>) `colData<-`(<SubsetSpatialExperiment>,<DataFrame>) `colData<-`(<SubsetSpatialExperiment>,<NULL>) `colData<-`(<SubsetSpatialExperiment>,<data.frame>) `colData<-`(<SubsetSpatialExperiment>,<ANY>) rowData(<SubsetTreeSummarizedExperiment>) colData(<SubsetTreeSummarizedExperiment>) `rowData<-`(<SubsetTreeSummarizedExperiment>) `colData<-`(<SubsetTreeSummarizedExperiment>,<DataFrame>) `colData<-`(<SubsetTreeSummarizedExperiment>,<NULL>) `colData<-`(<SubsetTreeSummarizedExperiment>,<data.frame>) `colData<-`(<SubsetTreeSummarizedExperiment>,<ANY>): rowData and colData of subsets in ExperimentSubset objects
reducedDim(<SubsetSingleCellExperiment>,<character>) reducedDim(<SubsetSingleCellExperiment>,<missing>) reducedDim(<SubsetSingleCellExperiment>,<numeric>) `reducedDim<-`(<SubsetSingleCellExperiment>,<character>) `reducedDim<-`(<SubsetSingleCellExperiment>,<missing>) `reducedDim<-`(<SubsetSingleCellExperiment>,<numeric>) reducedDims(<SubsetSingleCellExperiment>) `reducedDims<-`(<SubsetSingleCellExperiment>) reducedDim(<SubsetSpatialExperiment>,<character>) reducedDim(<SubsetSpatialExperiment>,<missing>) reducedDim(<SubsetSpatialExperiment>,<numeric>) `reducedDim<-`(<SubsetSpatialExperiment>,<character>) `reducedDim<-`(<SubsetSpatialExperiment>,<missing>) `reducedDim<-`(<SubsetSpatialExperiment>,<numeric>) reducedDims(<SubsetSpatialExperiment>) `reducedDims<-`(<SubsetSpatialExperiment>) reducedDim(<SubsetTreeSummarizedExperiment>,<character>) reducedDim(<SubsetTreeSummarizedExperiment>,<missing>) reducedDim(<SubsetTreeSummarizedExperiment>,<numeric>) `reducedDim<-`(<SubsetTreeSummarizedExperiment>,<character>) `reducedDim<-`(<SubsetTreeSummarizedExperiment>,<missing>) `reducedDim<-`(<SubsetTreeSummarizedExperiment>,<numeric>) reducedDims(<SubsetTreeSummarizedExperiment>) `reducedDims<-`(<SubsetTreeSummarizedExperiment>): Reduced dimensions of subsets in ExperimentSubset objects
`reducedDimNames<-`(): reducedDimNames<-
reducedDimNames(): reducedDimNames
altExp(<SubsetSingleCellExperiment>,<character>) altExp(<SubsetSingleCellExperiment>,<missing>) altExp(<SubsetSingleCellExperiment>,<numeric>) altExps(<SubsetSingleCellExperiment>) altExpNames(<SubsetSingleCellExperiment>) `altExpNames<-`(<SubsetSingleCellExperiment>,<character>) `altExpNames<-`(<SubsetSingleCellExperiment>,<ANY>) `altExp<-`(<SubsetSingleCellExperiment>,<character>) `altExp<-`(<SubsetSingleCellExperiment>,<missing>) `altExp<-`(<SubsetSingleCellExperiment>,<numeric>) `altExps<-`(<SubsetSingleCellExperiment>) altExp(<SubsetSpatialExperiment>,<character>) altExp(<SubsetSpatialExperiment>,<missing>) altExp(<SubsetSpatialExperiment>,<numeric>) altExps(<SubsetSpatialExperiment>) altExpNames(<SubsetSpatialExperiment>) `altExpNames<-`(<SubsetSpatialExperiment>,<character>) `altExpNames<-`(<SubsetSpatialExperiment>,<ANY>) `altExp<-`(<SubsetSpatialExperiment>,<character>) `altExp<-`(<SubsetSpatialExperiment>,<missing>) `altExp<-`(<SubsetSpatialExperiment>,<numeric>) `altExps<-`(<SubsetSpatialExperiment>) altExp(<SubsetTreeSummarizedExperiment>,<character>) altExp(<SubsetTreeSummarizedExperiment>,<missing>) altExp(<SubsetTreeSummarizedExperiment>,<numeric>) altExps(<SubsetTreeSummarizedExperiment>) altExpNames(<SubsetTreeSummarizedExperiment>) `altExpNames<-`(<SubsetTreeSummarizedExperiment>,<character>) `altExpNames<-`(<SubsetTreeSummarizedExperiment>,<ANY>) `altExp<-`(<SubsetTreeSummarizedExperiment>,<character>) `altExp<-`(<SubsetTreeSummarizedExperiment>,<missing>) `altExp<-`(<SubsetTreeSummarizedExperiment>,<numeric>) `altExps<-`(<SubsetTreeSummarizedExperiment>): Alternative experiments of subsets in ExperimentSubset objects
metadata(<SubsetRangedSummarizedExperiment>) `metadata<-`(<SubsetRangedSummarizedExperiment>) metadata(<SubsetSingleCellExperiment>) `metadata<-`(<SubsetSingleCellExperiment>) metadata(<SubsetSummarizedExperiment>) `metadata<-`(<SubsetSummarizedExperiment>) metadata(<SubsetSpatialExperiment>) `metadata<-`(<SubsetSpatialExperiment>) metadata(<SubsetTreeSummarizedExperiment>) `metadata<-`(<SubsetTreeSummarizedExperiment>): Metadata of subsets in ExperimentSubset objects