omicverse.utils.convert2symbol

omicverse.utils.convert2symbol(adata, scopes=None, subset=True)[source]

Convert Ensembl IDs in adata.var_names to official gene symbols.

Parameters:

  • adata (AnnData) – Input AnnData object whose var_names contain Ensembl gene or transcript IDs (e.g. ENSG*, ENSMUSG*, ENST*).

  • scopes (str, iterable, or None, optional) –

    Identifier type passed to convert2gene_symbol(). Common values are 'ensembl.gene' and 'ensembl.transcript'. If None, the scope is inferred from the first entry of adata.var_names:

    • ENSG* / ENSMUSG* → 'ensembl.gene'

    • ENST* / ENSMUST* → 'ensembl.transcript'

  • subset (bool, optional) – If True (default), genes that could not be converted are dropped from adata. If False, unconverted genes retain their original Ensembl ID.

Returns:

Updated AnnData with var_names replaced by official gene symbols. The original Ensembl IDs are preserved in adata.var['query'].

Return type:

AnnData

Raises:

Exception – If scopes is None and the gene IDs cannot be recognised as ensembl.gene or ensembl.transcript.

Examples

>>> adata = ov.utils.convert2symbol(adata)
>>> adata = ov.utils.convert2symbol(adata, subset=False)