cassiopeia.pp.filter_cells¶
- cassiopeia.pp.filter_cells(molecule_table, min_umi_per_cell=10, min_avg_reads_per_umi=2.0)[source]¶
Filter out cell barcodes that have too few UMIs or too few reads/UMI
- Parameters
- molecule_table :
DataFrameDataFrame A molecule table of cellBC-UMI pairs to be filtered
- min_umi_per_cell :
intint(default:10) Minimum number of UMIs per cell for cell to not be filtered
- min_avg_reads_per_umi :
floatfloat(default:2.0) Minimum coverage (i.e. average) reads per UMI in a cell needed in order for that cell not to be filtered
- molecule_table :
- Return type
- Returns
A filtered molecule table