dynamo.pp.convert2symbol
- dynamo.pp.convert2symbol(adata, scopes=None, subset=True)[source]
This helper function converts unofficial gene names to official gene names.
- Parameters:
adata (
AnnData) – an AnnData object.scopes (
Union[str,Iterable,None]) – scopes are needed when you use non-official gene name as your gene indices (or adata.var_name). This arugument corresponds to type of types of identifiers, either a list or a comma-separated fields to specify type of input qterms, e.g. “entrezgene”, “entrezgene,symbol”, [“ensemblgene”, “symbol”]. Refer to official MyGene.info docs (https://docs.mygene.info/en/latest/doc/query_service.html#available_fields) for full list of fields. Defaults to None.subset – whether to inplace subset the results. Defaults to True.
- Raises:
Exception – gene names in adata.var_names are invalid.
- Return type:
- Returns:
The updated AnnData object.