fix updating var with hvg multibatch

scverse · Dec 17, 2024 · 64551aa · 64551aa
1 parent 0704cac
commit 64551aa
Showing 1 changed file with 5 additions and 3 deletions.
diff --git a/src/rapids_singlecell/preprocessing/_hvg.py b/src/rapids_singlecell/preprocessing/_hvg.py
@@ -14,7 +14,7 @@
 
 from rapids_singlecell._compat import DaskArray, _meta_dense, _meta_sparse
 
-from ._qc import calculate_qc_metrics
+from ._qc import _basic_qc
 from ._utils import _check_gpu_X, _check_nonnegative_integers, _get_mean_var
 
 if TYPE_CHECKING:
@@ -434,8 +434,10 @@ def _highly_variable_genes_batched(
     for batch in batches:
         adata_subset = adata[adata.obs[batch_key] == batch]
 
-        calculate_qc_metrics(adata_subset, layer=layer)
-        filt = adata_subset.var["n_cells_by_counts"].to_numpy() > 0
+        X = _get_obs_rep(adata_subset, layer=layer)
+        _check_gpu_X(X, allow_dask=True)
+        _, _, _, n_cells_per_gene = _basic_qc(X=X)
+        filt = (n_cells_per_gene > 0).get()
         adata_subset = adata_subset[:, filt]
 
         hvg = _highly_variable_genes_single_batch(