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Adjust features filter in scPRINT #36

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Jan 20, 2025
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Adjust features filter in scPRINT #36

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3 changes: 1 addition & 2 deletions src/methods/scprint/script.py
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Original file line number Diff line number Diff line change
Expand Up @@ -41,8 +41,7 @@

print("\n>>> Preprocessing data...", flush=True)
preprocessor = Preprocessor(
# Lower this threshold for test datasets
min_valid_genes_id=1000 if input.n_vars < 2000 else 10000,
min_valid_genes_id=min(0.9 * adata.n_vars, 10000), # 90% of features up to 10,000
# Turn off cell filtering to return results for all cells
filter_cell_by_counts=False,
min_nnz_genes=False,
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