terra.harmonize_adata

terra.harmonize_adata(adata, gene_mapping_dict_file_path=None, gene_occurrence_count_file_path=None, gene_occurrence_count_filter_value=10, ensembl_release=111, species='human', min_genes_per_cell=10, min_cells_per_gene=10)

Harmonize an AnnData object prior to tokenization.

Parameters:

• adata (AnnData) – An unharmonized AnnData object.

• ensembl_release (int (default: 111)) – Ensembl release used to retrieve ensembl IDs.

• min_genes_per_cell (int (default: 10)) – Minimum amount of genes per cell for a cell not to be filtered.

Return type:

AnnData

Returns:

adata: A harmonized AnnData object.