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Assays of subsets in ExperimentSubset objects

Source: R/ExperimentSubset.R, R/SubsetRangedSummarizedExperiment.R, R/SubsetSingleCellExperiment.R, and 3 more
ExperimentSubset-assay.Rd

Get or set an assay of the main object or of a subset. Unlike the other methods, assay() and assay<- name the subset with i, not with subsetName.

assay(x, i) returns:

  • a main assay, when i is its name, as for the class x extends;

  • the subset's rows and columns of the assay it was made from, when i is a subset name. If the subset, or a subset it was made from, stored its own assay of that name with unlink, that assay is returned instead;

  • an assay as a subset sees it, when i is "subset/assay", or a subset name with subsetAssayName = "assay": either one stored in the subset, or one linked from its parent, cut to the subset's rows and columns.

assay(x, i) <- value stores value in a subset when i is "subset/assay", or a subset name with subsetAssayName, as setSubsetAssay does. A name with a "/" is read as "subset/assay" unless it is the name of a main assay, and a subset name without subsetAssayName is an error. Any other name stores a main assay.

Usage

# S4 method for class 'SubsetRangedSummarizedExperiment,character'
assay(x, i, withDimnames = TRUE, ...)

# S4 method for class 'SubsetRangedSummarizedExperiment,character'
assay(x, i, withDimnames = TRUE, ...) <- value

# S4 method for class 'SubsetSingleCellExperiment,character'
assay(x, i, withDimnames = TRUE, ...)

# S4 method for class 'SubsetSingleCellExperiment,character'
assay(x, i, withDimnames = TRUE, ...) <- value

# S4 method for class 'SubsetSummarizedExperiment,character'
assay(x, i, withDimnames = TRUE, ...)

# S4 method for class 'SubsetSummarizedExperiment,character'
assay(x, i, withDimnames = TRUE, ...) <- value

# S4 method for class 'SubsetSpatialExperiment,character'
assay(x, i, withDimnames = TRUE, ...)

# S4 method for class 'SubsetSpatialExperiment,character'
assay(x, i, withDimnames = TRUE, ...) <- value

# S4 method for class 'SubsetTreeSummarizedExperiment,character'
assay(x, i, withDimnames = TRUE, ...)

# S4 method for class 'SubsetTreeSummarizedExperiment,character'
assay(x, i, withDimnames = TRUE, ...) <- value

Arguments

x

An ExperimentSubset object.

i

character(1) The name of a main assay, a subset name, or "subset/assay".

withDimnames

logical(1) As for SummarizedExperiment: TRUE gives the assay returned the row and column names of the main object or the subset, and FALSE keeps the names stored with the assay, if any. When setting a main assay, passed on to the method of the class x extends. Default TRUE.

...
subsetAssayName

character(1) With a subset name in i, the name of the assay to get from or store in that subset. It is an error with any other i, including "subset/assay". Default NULL.

unlink

TRUE, FALSE or a character vector of assay names. When storing in a subset, store the assay even though the subset sees an assay of that name linked from its parent, with TRUE or a vector that contains its name, as for setSubsetAssay. It is an error when storing a main assay. Default FALSE.

For a main assay, other arguments are passed on to the method of the class x extends.

value

A matrix-like assay with the main object's dimensions, or, to store it in a subset, the subset's.

Value

assay() returns a matrix-like assay. assay<- returns x with the assay stored.

See also

getSubsetAssay, setSubsetAssay, assay

Examples

# an object with 10 genes and 20 cells
set.seed(1)
counts <- matrix(rpois(200, lambda = 5), nrow = 10)
rownames(counts) <- paste0("gene", 1:10)
colnames(counts) <- paste0("cell", 1:20)
es <- ExperimentSubset(list(counts = counts))
# a subset of the first 5 genes and the first 8 cells
es <- createSubset(es, subsetName = "first", rows = 1:5, cols = 1:8)
# the subset's 5 x 8 part of the counts
firstCounts <- assay(es, "first")
# store a new assay in the subset
assay(es, "first", subsetAssayName = "logcounts") <- log1p(firstCounts)
#> Storing assay inside subset 'first'.
# read it back
assay(es, "first/logcounts")
#>          cell1    cell2    cell3    cell4    cell5    cell6    cell7    cell8
#> gene1 1.609438 1.386294 2.302585 1.791759 2.079442 1.791759 2.197225 1.609438
#> gene2 1.609438 1.386294 1.386294 1.791759 1.945910 2.079442 1.609438 2.079442
#> gene3 1.791759 1.945910 1.945910 1.791759 2.079442 1.609438 1.791759 1.609438
#> gene4 2.197225 1.609438 1.386294 1.386294 1.791759 1.386294 1.609438 1.609438
#> gene5 1.386294 2.079442 1.609438 2.079442 1.791759 1.098612 1.945910 1.791759