I’d like to work with my SingleCellExperiment (sce) object in galaxy (HCA), but I’m not sure how to save it as a
“Serialized SingleCellExperiment in RDS format” ie. ‘rdata.sce’ data type.
For example, I’d like to run Scater CalculateCPM (or scEasy) , which expects this input format.
For my first try, I just ran saveRDS(sce) on my sce object - which of course didn’t work because the counts data is still on my local disk (see saveHDF5SummarizedExperiment: Save/load an HDF5-based SummarizedExperiment object in HDF5Array: HDF5 backend for DelayedArray objects). The scater script just seems to use readRDS (bioconductor-scater-scripts/scater-calculate-cpm.R at master · ebi-gene-expression-group/bioconductor-scater-scripts · GitHub)
Is there some smart function I should be calling to serialize the whole thing smartly into a single RDS file? The real dataset is big enough that I want to keep it in a sensible non-dense format.