Store a standalone experiment object back into a subset

Stores what a tool added to an object returned by getSubsetExperiment: new assays, rowData and colData columns, reducedDims, altExps and metadata.

Usage

setSubsetExperiment(x, subsetName, value, unlink = FALSE)

# S4 method for class 'SubsetRangedSummarizedExperiment'
setSubsetExperiment(x, subsetName, value, unlink = FALSE)

# S4 method for class 'SubsetSingleCellExperiment'
setSubsetExperiment(x, subsetName, value, unlink = FALSE)

# S4 method for class 'SubsetSummarizedExperiment'
setSubsetExperiment(x, subsetName, value, unlink = FALSE)

# S4 method for class 'SubsetSpatialExperiment'
setSubsetExperiment(x, subsetName, value, unlink = FALSE)

# S4 method for class 'SubsetTreeSummarizedExperiment'
setSubsetExperiment(x, subsetName, value, unlink = FALSE)

Arguments

x

Input ExperimentSubset object.

subsetName

character(1) The name of the subset.

value

An object of the main object's class (not a subclass or a parent class) with the subset's dimensions and the subset's row and column names, in the same order. A tool that drops rows or columns is followed by createSubset instead.

unlink

TRUE, FALSE or a character vector of assay names. Store assays of value that have the name of an assay linked from the subset's parent but different values, as with setSubsetAssay: with TRUE, every such assay; with a character vector, only those it names. An assay of an altExp is named "altExpName/assayName", such as "ADT/counts". Any other such assay, of the main object or an altExp, is an error, and nothing is stored. A message names each assay that is unlinked. Names of assays that are not linked, or unchanged, are ignored, so unlink = "decontXcounts" stores a changed decontXcounts but stops if counts was changed too. Default FALSE.

Value

Updated ExperimentSubset object. Linked assays that are in value hold the same values as what the subset sees (whatever their dimnames, type or class) are not stored, and neither are the main object's rowData and colData columns added by getSubsetExperiment. altExps are stored as altExp<- stores them (see ExperimentSubset-altExp): only the assays and data that differ from a linked altExp, and a linked altExp missing from value stays linked. Everything else in value replaces the subset's own data: an own assay, reducedDim, altExp or column that value no longer has is removed from the subset, except an assay another subset was made from, which is an error. Nothing else is stored: not row ranges, row and column trees, spatial coordinates, images, colPairs, rowPairs or mainExpName.

Examples

data(sce_chcl, package = "scds")
es <- ExperimentSubset(sce_chcl)
es <- createSubset(es, "subset1", rows = 1:100, cols = 1:50)
subset1 <- getSubsetExperiment(es, "subset1")
# add a reducedDim and a colData column to the standalone object
reducedDim(subset1, "random") <- matrix(rnorm(100), nrow = 50)
subset1$group <- rep(c("a", "b"), 25)
# and store them in the subset
es <- setSubsetExperiment(es, "subset1", subset1)
reducedDimNames(es, subsetName = "subset1")
#> [1] "random"