no slot of name "counts" for this object of class "Assay5" error message

[BartBryant]

thanks for developing loupeR, has worked great for all my Seurat objects to help share data to others

however, i have a seurat object where our collaborator removed doublets with 'singleCellTK'; however, now i get the error message

Error in select_assay(obj) :

no slot of name "counts" for this object of class "Assay5"

after running 'create_loupe_from_seurat( )' function from 'loupeR'.

seems 'singleCellTK' to filter doublets altered the structure of my SeuratObject, so what is the structure a SeuratObject needs to be in order to run loupeR?

thanks and let me know if you need more info

[esiegel]

By default loupeR looks for the counts matrix at assay$counts. It seems that the singleCellITK tool creates a new counts matrix at decontXcounts as can be seen here.

The error message should probably be updated and it should fail more gracefully.

For now you can get around this issue by directly calling create_loupe and passing in the appropriate parameters.