How to add loom assays to Seurat object: Error in UseMethod(generic = "as.sparse", object = x) : no applicable method for 'as.sparse' applied to an object of class "Assay"?

[denvercal1234GitHub]

Hi there,

I had loom objects for different samples generated by velocyto, and a Seurat object that had been fully analysed (with SCTransform clustering and UMAP etc).

I was able to concatenate my loom objects into 1 object and converted it to Seurat object, but this object has not been in anyway processed (e.g., normalise etc that are typically done in scVelo pipeline).

How might I add the ambiguous, matrix, spliced, unspliced to my Seurat GEX cluster object? Do I do as below?

test[["ambiguous"]] <- CreateAssayObject(counts = concat_adata_Seurat@assays$ambiguous)
test[["matrix"]] <- CreateAssayObject(counts = concat_adata_Seurat@assays$matrix)
test[["spliced"]] <- CreateAssayObject(counts = concat_adata_Seurat@assays$splice)

Doing this gave me error however "Error in UseMethod(generic = "as.sparse", object = x) : no applicable method for 'as.sparse' applied to an object of class "Assay""

Thank you for your help!

My Seurat GEX cluster object:

My loom-converted Seurat object:

Posted zhanghao-njmu/SCP#130

[AustinHartman]

It looks like you are providing full Assays to CreateAssayObject via the counts parameter. You should be able to edit your code to either of the following:

test[["ambiguous"]] <- concat_adata_Seurat@assays$ambiguous

test[["ambiguous"]] <- CreateAssayObject(counts = concat_adata_Seurat@assays$ambiguous@counts)