pegasus.get_filter_stats

pegasus.get_filter_stats(data, min_genes_before_filt=100)[source]

Calculate filtration stats on cell barcodes.

Parameters
  • data (pegasusio.MultimodalData) – Use current selected modality in data, which should contain one RNA expression matrix.

  • min_genes_before_filt (int, optional, default 100) – If raw data matrix is input, empty barcodes will dominate pre-filtration statistics. To avoid this, for raw matrix, only consider barcodes with at least <number> genes for pre-filtration condition.

Returns

df_cells – Data frame of stats on cell filtration.

Return type

pandas.DataFrame

Examples

>>> df = pg.get_filter_stats(data)