scanpy.queries.mitochondrial_genes

scanpy.queries.mitochondrial_genes(org, *, attrname='external_gene_name', host='www.ensembl.org', use_cache=False, chromosome='MT')

Mitochondrial gene symbols for specific organism through BioMart.

Parameters

org : str: Organism to query. Must be an organism in ensembl biomart. “hsapiens”, “mmusculus”, “drerio”, etc.
attrname : str (default: 'external_gene_name'): Biomart attribute field to return. Possible values include “external_gene_name”, “ensembl_gene_id”, “hgnc_symbol”, “mgi_symbol”, and “zfin_id_symbol”.
host : str (default: 'www.ensembl.org'): A valid BioMart host URL. Alternative values include archive urls (like “grch37.ensembl.org”) or regional mirrors (like “useast.ensembl.org”).
use_cache : bool (default: False): Whether pybiomart should use a cache for requests. Will create a .pybiomart.sqlite file in current directory if used.
chromosome : str (default: 'MT'): Mitochrondrial chromosome name used in BioMart for organism.

Return type

DataFrame

Returns

Dataframe containing identifiers for mitochondrial genes.

Examples

>>> import scanpy as sc
>>> mito_gene_names = sc.queries.mitochondrial_genes("hsapiens")
>>> mito_ensembl_ids = sc.queries.mitochondrial_genes("hsapiens", attrname="ensembl_gene_id")
>>> mito_gene_names_fly = sc.queries.mitochondrial_genes("dmelanogaster", chromosome="mitochondrion_genome")