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Name retrieval method for all subset assays in ExperimentSubset objects

Source: R/allGenerics.R, R/SubsetRangedSummarizedExperiment.R, R/SubsetSingleCellExperiment.R, and 3 more
subsetAssayNames.Rd

Retrieves the names of all the subsets as well as the subset assays.

Usage

subsetAssayNames(x, subsetName = NULL)

# S4 method for class 'SubsetRangedSummarizedExperiment'
subsetAssayNames(x, subsetName = NULL)

# S4 method for class 'SubsetSingleCellExperiment'
subsetAssayNames(x, subsetName = NULL)

# S4 method for class 'SubsetSummarizedExperiment'
subsetAssayNames(x, subsetName = NULL)

# S4 method for class 'SubsetSpatialExperiment'
subsetAssayNames(x, subsetName = NULL)

# S4 method for class 'SubsetTreeSummarizedExperiment'
subsetAssayNames(x, subsetName = NULL)

Arguments

x

ExperimentSubset Input ExperimentSubset object.

subsetName

character(1) If given, list the assays seen in this subset instead: its own assays and those linked from its parent. Default NULL.

Value

A vector containing the names of the subsets followed by each assay stored in a subset as "subset/assay", or, with subsetName, the names of the assays seen in that subset.

Examples

data(sce_chcl, package = "scds")
es <- ExperimentSubset(sce_chcl)
es <- createSubset(es, "subset1",
rows = c(10,11,50,56,98,99,102,105,109, 200),
cols = c(20,21,40,45,90,99,100,123,166,299),
parentAssay = "counts")
assay(es, "subset1",
subsetAssayName = "subset1pAssay") <- assay(es, "subset1")[,] + 1
#> Storing assay inside subset 'subset1'.
subsetAssayNames(es)
#> [1] "subset1"               "subset1/subset1pAssay"
subsetAssayNames(es, subsetName = "subset1")
#> [1] "counts"        "logcounts"     "subset1pAssay"