Seurat2SAHA on custom DB

[domjacri]

Custom assay names break Seurat 2 SAHA... consider fixing

SAHA_input = Seurat2SAHA(objf, output="Both")
Calculating Variable Features:
Storing 2000 variable features.
Calculating Average Expression:
Error in PseudobulkExpression.Seurat(object = object, assays = assays, :
None of the requested assays are present in the object

[richardmustaklem]

Updated, please close when confirming. Here is a template.

objf <- seurat_obj
# rename RNA assay to something custom
objf[["custom"]] <- objf[["RNA"]]
objf@assays$RNA <- NULL
DefaultAssay(objf) <- "custom"
Assays(objf)     
Seurat2SAHA(objf, output = "Both")  # should now work, using "custom" or anything