infercnvpy.io.genomic_position_from_biomart

infercnvpy.io.genomic_position_from_biomart#

infercnvpy.io.genomic_position_from_biomart(adata=None, *, adata_gene_id=None, biomart_gene_id='ensembl_gene_id', species='hsapiens', inplace=True, **kwargs)#

Get genomic gene positions from ENSEMBL Biomart.

Parameters:

  • adata (Optional[AnnData] (default: None)) – Adds the genomic positions to adata.var. If adata is None, returns a data frame with the genomic positions instead.

  • adata_gene_id (Optional[str] (default: None)) – Column in adata.var that contains (ENSMBL) gene IDs. If not specified, use adata.var_names.

  • biomart_gene_id (default: 'ensembl_gene_id') – The biomart column to use as gene identifier. Typically this would be ensembl_gene_id or hgnc_symbol, but could be different for other species.

  • inplace (bool (default: True)) – If True, add the annotations directly to adata, otherwise return a dataframe.

  • **kwargs – passed on to scanpy.queries.biomart_annotations()

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