simplifyToSCE: Simplify a list to a single SingleCellExperiment

In LTLA/SingleCellExperiment: S4 Classes for Single Cell Data

Simplify a list to a single SingleCellExperiment

Description

Simplify a list of SingleCellExperiment, usually generated by applySCE on main and alternative Experiments, into a single SingleCellExperiment containing some of the results in its altExps.

Usage

simplifyToSCE(results, which.main, warn.level = 2)

Arguments

results	A named list of SummarizedExperiment or SingleCellExperiment objects.
which.main	Integer scalar specifying which entry of results contains the output generated from the main Experiment. If NULL or a vector of length zero, this indicates that no entry was generated from the main Experiment. Defaults to the unnamed entry of results.
warn.level	Integer scalar specifying the type of warnings that can be emitted.

Details

Each entry of results should be a SummarizedExperiment with the same number and names of the columns. There should not be any duplicate entries in names(results), as the names are used to represent the names of the alternative Experiments in the output. If which.main is a scalar, the corresponding entry of results should be a SingleCellExperiment. Failure to meet these conditions may result in a warning or error depending on warn.level.

The type of warnings that are emitted can be controlled with warn.level. If warn.level=0, no warnings are emitted. If warn.level=1, all warnings are emitted except for those related to results not being of the appropriate class. If warn.level=2, all warnings are emitted, and if warn.level=3, warnings are promoted to errors.

Value

A SingleCellExperiment corresponding to the entry of results generated from the main Experiment. All results generated from the alternative Experiments of x are stored in the altExps of the output.

If no main Experiment was used to generate results, an empty SingleCellExperiment is used as a container for the various altExps.

If simplification could not be performed, NULL is returned with a warning (depending on warn.level.

Author(s)

Aaron Lun

See Also

applySCE, where this function is used when SIMPLIFY=TRUE.

Examples

ncells <- 100
u <- matrix(rpois(20000, 5), ncol=ncells)
sce <- SingleCellExperiment(assays=list(counts=u))
altExp(sce, "BLAH") <- SingleCellExperiment(assays=list(counts=u*10))
altExp(sce, "WHEE") <- SingleCellExperiment(assays=list(counts=u*2))

# Setting FUN=identity just extracts each piece:
results <- applySCE(sce, FUN=identity, SIMPLIFY=FALSE)
results

# Simplifying to an output that mirrors the structure of 'sce'.
simplifyToSCE(results)

LTLA/SingleCellExperiment documentation built on March 28, 2024, 7:47 a.m.