Take a subset out as a standalone experiment object

Returns a subset as an object of the main object's class (for example a SingleCellExperiment), so that any tool written for that class can be run on the subset. Store what the tool added with setSubsetExperiment.

Usage

getSubsetExperiment(x, subsetName, parentData = TRUE)

# S4 method for class 'SubsetRangedSummarizedExperiment'
getSubsetExperiment(x, subsetName, parentData = TRUE)

# S4 method for class 'SubsetSingleCellExperiment'
getSubsetExperiment(x, subsetName, parentData = TRUE)

# S4 method for class 'SubsetSummarizedExperiment'
getSubsetExperiment(x, subsetName, parentData = TRUE)

# S4 method for class 'SubsetSpatialExperiment'
getSubsetExperiment(x, subsetName, parentData = TRUE)

# S4 method for class 'SubsetTreeSummarizedExperiment'
getSubsetExperiment(x, subsetName, parentData = TRUE)

Arguments

x

Input ExperimentSubset object.

subsetName

character(1) The name of the subset.

parentData

logical(1) Include the main object's rowData and colData columns for the subset's rows and columns, as with parentRowData and parentColData. They are marked so that setSubsetExperiment doesn't store copies of them. A subset's own column hides the main object's column of the same name, with a message if their values differ. Default TRUE.

Value

An object of the main object's class with the subset's rows and columns and row and column names. Its assays are every assay the subset sees, its own and those linked from its parent, under their names, with the subset's primary assay first. Its rowData and colData are the subset's, after the main object's columns if parentData = TRUE. Its altExps are every altExp the subset sees, its own and those linked from the main object or a parent subset, cut to its columns (see ExperimentSubset-altExp). Its reducedDims and metadata are the subset's. Everything else, such as row ranges, row and column trees, spatial coordinates, images, colPairs and rowPairs, comes from the main object.

Examples

data(sce_chcl, package = "scds")
es <- ExperimentSubset(sce_chcl)
es <- createSubset(es, "subset1", rows = 1:100, cols = 1:50)
subset1 <- getSubsetExperiment(es, "subset1")
subset1
#> class: SingleCellExperiment 
#> dim: 100 50 
#> metadata(0):
#> assays(2): counts logcounts
#> rownames(100): C12orf73 RNU6-1256P ... GABRA2 RP11-563K23.1
#> rowData names(1): gene
#> colnames(50): CTGCTGTCAGGGTATG CAGTCCTTCGGTTAAC ... ACACTGATCGAATCCA
#>   ACGTCAACAGGTCGTC
#> colData names(11): nGene nUMI ... ident doublet_true_labels
#> reducedDimNames(0):
#> mainExpName: NULL
#> altExpNames(0):