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satijalab / seurat-object

https://satijalab.github.io/seurat-object/
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SeuratObject::merge - collapse option mentioned in documentation but not yet implemented #175

Open adam-cornwell opened 10 months ago

adam-cornwell commented 10 months ago

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 commented 10 months ago

I meet the same problem

aditisk commented 7 months ago

Same here, anyone found a solution yet ? Thanks.

bbimber commented 5 months ago

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 commented 2 months ago

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