SeuratObject::merge - collapse option mentioned in documentation but not yet implemented

[adam-cornwell]

Seurat and SeuratObject 5.0.1 installed from CRAN.
Attempting to merge SeuratObjects with "collapse=TRUE" results in error "Collapsing layers is not yet supported". I can see also in the current GitHub source that the functionality is not yet implemented. However, the documentation in the current release version (from "?merge.Seurat") does not indicate that the option does not yet exist and that it will throw an error.

[zty1161103901]

I meet the same problem

[aditisk]

Same here, anyone found a solution yet ? Thanks.

[bbimber]

We also hit this problem. I had to write code to undo the layer splitting (which is unfortunately now the default) because many other tools that read seurat objects dont properly interact with layers.

Are there plans to support collapse=FALSE for merge()?

[andrei-stoica26]

seuratObj[["RNA"]] <- JoinLayers(seuratObj[["RNA"]]) should work for this task.