xchrom.pp.filter_multiome_data

xchrom.pp.filter_multiome_data(ad_rna: AnnData, ad_atac: AnnData, filter_ratio: float = 0.05, species: Literal['mouse', 'human'] = 'human', min_genes: int = 0, min_cells: int = 0) → Tuple[AnnData, AnnData][source]

Filter multiome RNA and ATAC data based on expression/accessibility thresholds and chromosomes

Parameters:

  • ad_rna (anndata.AnnData) – RNA expression data (cells x genes)

  • ad_atac (anndata.AnnData) – ATAC accessibility data (cells x peaks)

  • filter_ratio (float, default is 0.05) – Minimum ratio of cells in which a gene/peak should be expressed/accessible

  • species (str, default is 'mouse') – Species name to determine chromosome filtering. Supports ‘mouse’ and ‘human’

  • min_genes (int, default is 0) – Minimum number of genes expressed per cell

  • min_cells (int, default is 0) – Minimum number of cells expressing each gene

Returns:

  • ad_rna_filtered (anndata.AnnData) – Filtered RNA data

  • ad_atac_filtered (anndata.AnnData) – Filtered ATAC data

Examples

>>> import xchrom as xc
>>> ad_rna, ad_atac = xc.pp.filter_multiome_data(
...     ad_rna=ad_rna,
...     ad_atac=ad_atac,
...     species='mouse',
...     filter_ratio=0.05,
...     min_genes=0,
...     min_cells=0
... )