Comments (4)
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.
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@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?
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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.
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Yes, I am getting an output and the data is interpretable. Thanks!
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Related Issues (20)
- Error in `generate_info_tables`
- Warning message in `predict_ligand_activities`
- `generate_prioritization_tables` warnings and documentation
- Error when passing the recorrect_umi argument in get_lfc_celltype HOT 1
- Error in WhichCells.Seurat(object = object, idents = ident.2) : Cannot find the following identities in the object: Adjacent HOT 1
- Error in `Idents<-`: ! 'value' must be a factor or vector HOT 3
- Different results running. the same. code in different version. of HOT 6
- Protein complex HOT 1
- Function generate_info_tables return an error HOT 3
- Low AUPR values in analyses HOT 4
- RankActiveLigands Error
- Can NicheNet be used for analyzing three groups? HOT 1
- Parallelization error when optimizing parameters for NicheNet HOT 4
- How is the Ligand-Target-Matrix generated? HOT 2
- Receiver cells in differential analysis HOT 1
- when sender cell type is only one, HOT 1
- Only activating interactions or also repressing? HOT 1
- Naming convention in prioritization table
- Change error in `alias_to_symbol_seurat()` to warning
- discrepancy in results output HOT 2
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