cell_type not found when subsetting object

neurorestore / Libra

MIT License

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cell_type not found when subsetting object #15

Open MjelleLab opened 2 years ago

MjelleLab commented 2 years ago

When running my whole Seurat object, run_de works fine. When I subset the object to contain only one cell type I get cell_type not found. What is the reason for this? I want to subset before running run_de to set different threshold for my cells types (High vs Low)

jordansquair commented 2 years ago

Strange - can you send me a sample of the data? (email on profile).

MjelleLab commented 2 years ago

Error was related to number of cells. Setting a filter of min 100 cells solved it.

yecotoo commented 2 months ago

libra_result = run_de(expr,meta = meta,

replicate_col = "orig.ident",
cell_type_col = "seurat_clusters",
label_col = "RNA_snn_res.0.25",
input_type = "scRNA",
de_family = 'pseudobulk',
de_method = 'edgeR',
de_type = 'LRT',
min_cells = 50,
min_reps = 2,
n_threads = 4
) Must group by variables found in .data. ✖ Column cell_type is not found. HOW TO FIX IT?