scFates.pp.filter_cells#
- scFates.pp.filter_cells(adata, device='cpu', p_level=None, subset=True, plot=False, copy=False)#
Filter cells using on gene/molecule relationship.
Code has been translated from pagoda2 R function gene.vs.molecule.cell.filter.
- Parameters:
- adata
AnnData Annotated data matrix.
- device default:
'cpu' Run gene and molecule counting on either cpu or on gpu.
- p_level default:
None Statistical confidence level for deviation from the main trend, used for cell filtering (default=min(1e-3,1/adata.shape[0]))
- subset default:
True if False, add a column outlier in adata.obs, otherwise subset the adata.
- plot default:
False Plot the molecule distribution and the gene/molecule dependency fit.
- copy default:
False Return a copy instead of writing to adata.
- adata
- Returns:
adata : anndata.AnnData if copy=True and subset=True it returns subsetted (removing outliers) or else add fields to adata:
- .obs[‘outlier’]
whether a cell is an outlier.