tacco.tools.run_orthology_converter

run_orthology_converter(adata, source_tax_id, target_tax_id=None, target_gene_symbols=None, use_synonyms=True)[source]

Run orthology conversion between species using MGI homology information information (Mouse Genome Informatics Web Site, http://www.informatics.jax.org/homology.shtml). The function works on the var.index of the adata and assumes to find gene symbols there.

Parameters:

  • adata – An AnnData containing the data to convert. If None, return an AnnData containing the conversion matrix.

  • source_tax_id – The NCBI taxonomy ID of the source data. Some strings can be used as aliases of their taxonomy IDs (e.g. ‘human’=9606 and ‘mouse’=10090).

  • target_tax_id – The target NCBI taxonomy ID. Some strings can be used as aliases of their taxonomy IDs (e.g. ‘human’=9606 and ‘mouse’=10090). If None, convert to the common MGI “DB class key”/”HomoloGene ID” (recommended, as this avoids extra ambuigities in multi-to-multi mappings).

  • target_gene_symbols – The gene symbols appearing in the target data. Supplying this can make a difference if the symbols appearing there are contained in the “Synonyms” column of the homology information. Synonyms are unambiguously taken care of on the source side.

  • use_synonyms – Whether to use the “Synonyms” column from the homology information.

Returns:

Returns a AnnData containing the result of the orthology conversion.