how to get layers info after running scDblFinder
IrinaVKuznetsova opened this issue · comments
Hi,
I'd like to clarify how do I get a Seurat v.5 object back with all layers information after running scDblFinder function? As we get all layers merged and saved under assays(2): counts logcounts.
Option 1 - to use split
seurat[["RNA"]] <- split(seurat[["RNA"]], f = "orig.ident")
error: ! Not enough splits for this assay
Option 2
- read Seurat object v.5 (with layers, and doublets were not removed
- Read Seurat object where doublets were removed (Seurat v.3 NO layers info)
- Subset 1) to 2)
- Add all info generated by scDblFinder to 3)
apology if I missed an easier way of coming back to Seurat v.5 with layers after removing doublets.
Thanks
Hi,
I don't really understand your question.
The only thing scDblFinder adds to the input object are the colData
columns, e.g. scDblFinder.score
and scDblFinder.class
. These you can simply transfer to your original Seurat object as explained in the vignette.
If that doesn't address your question, please clarify it / what you need.
plger
Will close this issue unless you want to clarify your question.