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"
... )