scvelo.pp.filter_genes¶
-
scvelo.pp.
filter_genes
(data, min_counts=None, min_cells=None, max_counts=None, max_cells=None, min_counts_u=None, min_cells_u=None, max_counts_u=None, max_cells_u=None, min_shared_counts=None, min_shared_cells=None, retain_genes=None, copy=False)¶ Filter genes based on number of cells or counts.
Keep genes that have at least min_counts counts or are expressed in at least min_cells cells or have at most max_counts counts or are expressed in at most max_cells cells. Only provide one of the optional parameters min_counts, min_cells, max_counts, max_cells per call.
- Parameters
- data :
AnnData
, np.ndarray, sp.spmatrix The (annotated) data matrix of shape n_obs × n_vars. Rows correspond to cells and columns to genes.
- min_counts : int, optional (default: None)
Minimum number of counts required for a gene to pass filtering.
- min_cells : int, optional (default: None)
Minimum number of cells expressed required for a gene to pass filtering.
- max_counts : int, optional (default: None)
Maximum number of counts required for a gene to pass filtering.
- max_cells : int, optional (default: None)
Maximum number of cells expressed required for a gene to pass filtering.
- min_counts_u : int, optional (default: None)
Minimum number of unspliced counts required for a gene to pass filtering.
- min_cells_u : int, optional (default: None)
Minimum number of unspliced cells expressed required to pass filtering.
- max_counts_u : int, optional (default: None)
Maximum number of unspliced counts required for a gene to pass filtering.
- max_cells_u : int, optional (default: None)
Maximum number of unspliced cells expressed required to pass filtering.
- min_shared_counts : int, optional (default: None)
Minimum number of counts (both unspliced and spliced) required for a gene.
- min_shared_cells : int, optional (default: None)
Minimum number of cells required to be expressed (both unspliced and spliced).
- retain_genes : list, optional (default: None)
List of gene names to be retained independent of thresholds.
- copy : bool, optional (default: False)
Determines whether a copy is returned.
- data :
- Returns
Filters the object and adds n_counts to adata.var.