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
simplifyToSCE(results, which.main, warn.level = 2)
A named list of SummarizedExperiment or SingleCellExperiment objects.
Integer scalar specifying which entry of
Integer scalar specifying the type of warnings that can be emitted.
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.
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
The type of warnings that are emitted can be controlled with
warn.level=0, no warnings are emitted.
warn.level=1, all warnings are emitted except for those related to
results not being of the appropriate class.
warn.level=2, all warnings are emitted, and if
warn.level=3, warnings are promoted to errors.
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
If simplification could not be performed,
NULL is returned with a warning (depending on
applySCE, where this function is used when
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)
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