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
Run gene and molecule counting on either cpu or on gpu.
- p_level
Statistical confidence level for deviation from the main trend, used for cell filtering (default=min(1e-3,1/adata.shape[0]))
- subset
if False, add a column outlier in adata.obs, otherwise subset the adata.
- plot
Plot the molecule distribution and the gene/molecule dependency fit.
- copy
Return a copy instead of writing to adata.
- adata :
- Returns
adata – 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.
- Return type