cellink.tl.external.load_roadmap_links

cellink.tl.external.load_roadmap_links(roadmap_file, tissue=None, eid_map_file=None)

Load Roadmap enhancer-gene links from the combined all-tissue file.

The actual file in the GCS bucket is RoadmapUABCannot_regions_to_genes.txt.gz, a single combined file for all tissues. Per-tissue files (Roadmap_BLD_E.txt.gz etc.) do not exist in the bucket; cellink filters the combined file here instead.

Parameters:

• roadmap_file (str | Path) – Path to RoadmapUABCannot_regions_to_genes.txt.gz, downloaded by download_sclinker_enhancer_links().

• tissue (str | None (default: None)) – Tissue code to filter to (e.g. "BLD"). If None, returns all rows. Uses Roadmap_map_EID_names.txt (eid_map_file) to match EIDs to tissue names. If eid_map_file is None, the tissue filter is applied as a case-insensitive substring match on the EID/tissue column.

• eid_map_file (str | Path | None (default: None)) – Path to Roadmap_map_EID_names.txt for EID→tissue mapping. Only used when tissue is not None.

Return type:

DataFrame

Returns:

pd.DataFrame with columns: chr, start, end, Gene, EID, activity (score).