decoupler.op.translate

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decoupler.op.translate#

decoupler.op.translate(net, columns=None, target_organism='mouse', min_evidence=3, one_to_many=5, verbose=False)#

Translates gene symbols from human to a target organism using the HCOP database.

Check which organisms are available with decoupler.op.show_organisms.

HCOP is a composite database combining data from various orthology resources. It provides a comprehensive set of orthologs among human, mouse, and rat, among many other species.

If you use this function, please reference the original HCOP paper: - Yates, B., Gray, K.A., Jones, T.E. and Bruford, E.A., 2021. Updates to HCOP: the HGNC comparison of orthology predictions tool. Briefings in Bioinformatics, 22(6), p.bbab155.

For more information, please visit the HCOP website: https://www.genenames.org/tools/hcop/, or the HCOP help page for bulk download details: https://www.genenames.org/help/hcop/

Parameters:

  • net (DataFrame) – Dataframe in long format. Must include source and target columns, and optionally a weight column.

  • columns (str | list | None (default: None)) – Column or columns of net to translate.

  • target_organism (str (default: 'mouse')) – Organism to translate to.

  • min_evidence (int (default: 3)) – Minimum number of evidences to keep the interaction, where evidence is the number of orthology resources supporting the interaction.

  • one_to_many (int (default: 5)) – Maximum number of orthologs allowed per gene.

Return type:

DataFrame

Returns:

Translated net.

Example

import decoupler as dc

ct = dc.op.collectri()
mouse_ct = dc.op.translate(ct, target_organism="mouse")
mouse_ct
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