| Environment | Status |
|---|---|
| BioC-release |  |
| BioC-devel |  |
The alabaster.sce package implements methods for saving and loading SingleCellExperiment objects under the alabaster framework.
It provides a language-agnostic method for serializing reduced dimensions and alternative experiments along with the usual bits and pieces from the SummarizedExperiment parent class.
To get started, install the package and its dependencies from Bioconductor:
# install.packages("BiocManager")
BiocManager::install("alabaster.sce")In the example below, we save a SingleCellExperiment object to file:
library(SingleCellExperiment)
example(SingleCellExperiment, echo=FALSE) # can't be bothered to copy it here.
sce
## class: SingleCellExperiment
## dim: 200 100
## metadata(0):
## assays(2): counts logcounts
## rownames: NULL
## rowData names(0):
## colnames: NULL
## colData names(0):
## reducedDimNames(2): PCA tSNE
## mainExpName: NULL
## altExpNames(0):
library(alabaster.sce)
tmp <- tempfile()
saveObject(sce, tmp)
roundtrip <- readObject(tmp)
class(roundtrip)
## [1] "SingleCellExperiment"
## attr(,"package")
## [1] "SingleCellExperiment"