get_expressed_genes() with Integration Workflow about nichenetr

[browaeysrobin]

Hi @uberholzer

I think this is not an error, but just a warning. Can you check this?
But to use the RNA slot, you can change the parameter assay_oi of the get_expressed_genes() function to assay_oi = RNA (it might be that you need to reinstall nichenetr to enable this though). This will use the RNA slot to define expressed genes instead of the integrated slot. The set default assay of the Seurat object does not matter here.

[uberholzer]

@browaeysrobin I am still getting the error even after re-installing nichnetr.

Here is the block of code I am running:

CTOI <- "pDC"
receiver = c("pDC")
Idents(object=seuratObj) <- "celltype_fine"
DefaultAssay(seuratObj) <- "RNA"
expressed_genes_receiver = get_expressed_genes(receiver, seuratObj, pct = 0.10,assay_oi = "RNA")
background_expressed_genes = expressed_genes_receiver %>% .[. %in% rownames(ligand_target_matrix)]
sender_celltypes = c("AM", "Mixed T", "Club cell", "Proliferating T", "Ciliated cell",
                     "Neutrophil", "mDC", "NK", "Proliferating Plasma Cell", "Plasma cell", "Mature B", "pDC", "Mast cell")
list_expressed_genes_sender = sender_celltypes %>% unique() %>% lapply(get_expressed_genes, seuratObj, 0.10)
expressed_genes_sender = list_expressed_genes_sender %>% unlist() %>% unique()

Should I assume the function is working properly on the RNA assay?

[browaeysrobin]

Hi @uberholzer

Do you get output for expressed_genes_receiver ? If yes then get_expressed_genes() just gives a warning and not an error.
I think it will just be a warning and everything is working properly on the RNA assay.

[uberholzer]

Yes, I am getting an output and the data is interpretable. Thanks!