A FunctionalSingleCellExperiment is implemented as a MultiAssayExperiment with one or more SingleCellExperiments (sce). One of these is a single-cell mRNA sequencing experiment that defines mRNA counts for single cells. Other sces include functional data from haircut.




a list mapping experiment names to SingleCellExperiments created by an create_ function.


MultiAssayExperiment containing one or more SingleCellExperiment.


# this is identical to the `fsce_small` data set: create_fsce( list( rnaseq = create_sce_rnaseq(scrunchy_data("mrna/")), haircut = create_sce_haircut(scrunchy_data("haircut/")) ) )
#> Loading sc-rnaseq matrix files: /home/travis/R/Library/scrunchy/extdata/mrna/
#> Loading haircut matrix files: /home/travis/R/Library/scrunchy/extdata/haircut/
#> A FunctionalSingleCellExperiment object of 2 listed #> experiments with user-defined names and respective classes. #> Containing an ExperimentList class object of length 2: #> [1] rnaseq: SingleCellExperiment with 9462 rows and 250 columns #> [2] haircut: SingleCellExperiment with 426 rows and 250 columns #> Features: #> experiments() - obtain the ExperimentList instance #> colData() - the primary/phenotype DFrame #> sampleMap() - the sample availability DFrame #> `$`, `[`, `[[` - extract colData columns, subset, or experiment #> *Format() - convert into a long or wide DFrame #> assays() - convert ExperimentList to a SimpleList of matrices