as.SingleCellExperiment Fails in Seurat_4.0.2

[bbimber]

Hello,

I'm seeing one warning and two errors in R 4.1, Seurat_4.0.2, and SeuratObject_4.0.1. The most severe is w/ as.SingleCellExperiment. Here is a repro

# Create dummy object:
mat <- matrix(1:100, ncol = 10)
colnames(mat) <- LETTERS[1:10]
rownames(mat) <- LETTERS[1:10]
  
# this works, but prints the warning "Warning: The following arguments are not used: row.names"
# I pointed this issue out with code pointers here: https://github.com/mojaveazure/seurat-object/issues/13
seuratObj <- Seurat::CreateSeuratObject(mat)
  

and then try this:

  sce <- as.SingleCellExperiment(seuratObj)

which gives:

Error in value[3L] :
invalid subscript 'e' in 'altExp(, type="character", ...)':
'RNA' not in 'altExpNames()'

I assume this has to do w/ trying to make as.SingleCellExperiment work with multiple assays in the object? The problem is here:

for (assayn in assay){
	# This fails if you try to swap the active experiment. 
	sce <- SingleCellExperiment::swapAltExp(x = sce, name = assayn, saved = orig.exp.name)
	SummarizedExperiment::rowData(x = sce) <- S4Vectors::DataFrame(x[[assayn]][[]])
	sce <- SingleCellExperiment::swapAltExp(x = sce, name = orig.exp.name, saved = assayn)
}