cellink.tl.external.load_gene_annotation

cellink.tl.external.load_gene_annotation(gene_annotation_file=None, gene_id_type='hgnc', data_home=None, refresh=False)

Load gene TSS/TES coordinates for the 100 kb window S2G strategy.

Calls get_gene_annotation() to locate or generate the file from Ensembl BioMart, then reads it into a DataFrame.

Parameters:

• gene_annotation_file (str | Path | None (default: None)) – Explicit path to an existing coord file. Passed to get_gene_annotation() as path.

• gene_id_type ("ensembl" | "hgnc") – Which identifier is in the GENE column — must match your data. Default is "ensembl" because sc-linker AnnData objects typically have ENSG var_names.

• data_home (str | Path | None (default: None)) – Override for the cellink data directory.

• refresh (bool (default: False)) – If True, re-query BioMart even if cached files exist.

Return type:

DataFrame

Returns:

pd.DataFrame Columns: GENE, CHR, START, END.