Subset creation method for ExperimentSubset objects

Create a subset from an already available assay in the input ExperimentSubset object by specifying the rows and columns to include in the subset.

Usage

createSubset(x, subsetName, rows = NULL, cols = NULL, parentAssay = NULL)

# S4 method for class 'SubsetRangedSummarizedExperiment'
createSubset(x, subsetName, rows = NULL, cols = NULL, parentAssay = NULL)

# S4 method for class 'SubsetSingleCellExperiment'
createSubset(x, subsetName, rows = NULL, cols = NULL, parentAssay = NULL)

# S4 method for class 'SubsetSummarizedExperiment'
createSubset(x, subsetName, rows = NULL, cols = NULL, parentAssay = NULL)

# S4 method for class 'SubsetSpatialExperiment'
createSubset(x, subsetName, rows = NULL, cols = NULL, parentAssay = NULL)

# S4 method for class 'SubsetTreeSummarizedExperiment'
createSubset(x, subsetName, rows = NULL, cols = NULL, parentAssay = NULL)

Arguments

x

ExperimentSubset Specify the object from which a subset should be created. Use ExperimentSubset() first to convert another experiment object.

subsetName

character(1) Specify the name of the subset to create.

rows

numeric or character vector. Specify the rows to include in this subset. If missing or NULL, all rows are included in the subset. Default NULL.

cols

numeric or character vector. Specify the columns to include in this subset. If missing or NULL, all columns are included in the subset. Default NULL.

parentAssay

character(1) Specify the parent assay of the subset: the name of a main assay, of a subset, or of an assay seen in a subset written as "subset/assay". If NULL, the first available main assay will be marked as parent. Default NULL.

Value

An ExperimentSubset object that now contains the newly created 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")
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(1): subset1
#> subsetAssays(1): subset1