ExperimentSubset constructor

This constructor function sets up an ExperimentSubset object from a SummarizedExperiment, RangedSummarizedExperiment, SingleCellExperiment, TreeSummarizedExperiment or SpatialExperiment object, or from a named list of assay matrices. A subset can also be created directly by passing a named list to the subset parameter, with elements named subsetName, rows, cols and parentAssay.

Usage

ExperimentSubset(
  x,
  subset = list(subsetName = NA, rows = NA, cols = NA, parentAssay = NA)
)

Arguments

x

An experiment object of one of the five supported classes, or a named list of assay matrices, which is passed to the SingleCellExperiment constructor as its assays. An object of a subclass of a supported class is converted as the class it extends, with a warning: the slots and methods that the subclass adds are not kept. An object that is already an ExperimentSubset is returned as is, with the subset from subset, if given.

subset

A named list to create a subset from within the constructor, with elements subsetName and, optionally, rows, cols and parentAssay. Leave out rows, cols or parentAssay, or set them to NULL, to use all rows, all columns or the first assay. The default, a list of NA values, creates no subset; an NA in a list you supply is an error.

Value

An object of the matching Subset* class, for example a SubsetSingleCellExperiment for a SingleCellExperiment or a list of assays. For an ExperimentSubset object, the same object, with the new subset if subset is given.

See also

ExperimentSubset, the class every Subset* class extends, for testing whether an object is an ExperimentSubset.

Examples

data(sce_chcl, package = "scds")
es <- ExperimentSubset(sce_chcl)
es
#> class: SubsetSingleCellExperiment 
#> dim: 2000 2000 
#> metadata(0):
#> assays(2): counts logcounts
#> rownames(2000): C12orf73 RNU6-1256P ... FOXF1 PRR3
#> rowData names(1): gene
#> colnames(2000): CTGCTGTCAGGGTATG CAGTCCTTCGGTTAAC ... GATGCTATCAGCAACT
#>   ATTTCTGGTGATGATA
#> colData names(11): nGene nUMI ... ident doublet_true_labels
#> reducedDimNames(0):
#> mainExpName: NULL
#> altExpNames(0):
#> subsets(0): 
#> subsetAssays(0):