Make a SingleCellExperiment object

Make a SingleCellExperiment object

Usage

makeSingleCellExperiment(..., reducedDims = S4Vectors::SimpleList())

Arguments

...

Passthrough arguments to makeSummarizedExperiment().

reducedDims

SimpleList. List containing matrices of cell coordinates in reduced space.

Value

SingleCellExperiment.

Note

Updated 2022-03-02.

See also

• AcidExperiment::makeSummarizedExperiment().

• SingleCellExperiment::altExps(), which has replaced the now defunct isSpike method for setting spike-in transcripts.

Examples

data(SingleCellExperiment_splatter, package = "AcidTest")

## SimpleList ====
object <- SingleCellExperiment_splatter
args <- list(
    "assays" = SummarizedExperiment::assays(object),
    "rowRanges" = SummarizedExperiment::rowRanges(object),
    "colData" = SummarizedExperiment::colData(object),
    "metadata" = S4Vectors::metadata(object),
    "reducedDims" = SingleCellExperiment::reducedDims(object)
)
sce <- do.call(what = makeSingleCellExperiment, args = args)
print(sce)
#> class: SingleCellExperiment 
#> dim: 100 400 
#> metadata(3): date sessionInfo wd
#> assays(1): counts
#> rownames(100): gene001 gene002 ... gene099 gene100
#> rowData names(10): broadClass description ... ncbiGeneId seqCoordSystem
#> colnames(400): cell001 cell002 ... cell399 cell400
#> colData names(1): sampleId
#> reducedDimNames(0):
#> mainExpName: NULL
#> altExpNames(0):