cellink.resources.get_eqtl_catalog_dataset_associations

cellink.resources.get_eqtl_catalog_dataset_associations(dataset_id, data_home=None, refresh=False, return_path=False, region=None, **params)

Retrieve cis-QTL summary statistics for one eQTL Catalogue dataset.

Parameters:

• dataset_id (str) – eQTL Catalogue dataset ID (e.g., "QTD000625", OneK1K Treg memory).

• data_home (str or Path, optional) – Directory to store cached files. Defaults to user data directory.

• refresh (bool, default=False) – If True, ignore cached data and re-fetch.

• return_path (bool, default=False) – If True, return the local cached file path instead of a DataFrame. Only meaningful for a whole-dataset download (region=None).

• region (str or sequence of str, optional) – One or more regions in tabix syntax ("6:89900000-90300000"), fetched with a remote range query instead of downloading the file. Chromosomes are named without a ``chr`` prefix and coordinates are GRCh38. Strongly recommended: a single dataset’s full summary statistics are ~1.4 GB.

• **params (Any) – Post-hoc row filters applied to the result as column=value, e.g. gene_id="ENSG00000112182" (BACH2) or rsid="rs72928038".

Return type:

DataFrame | Path

Returns:

pd.DataFrame or Path Summary statistics, or the cached file path when return_path=True.

Notes

The eQTL Catalogue REST API this function previously used (https://www.ebi.ac.uk/eqtl/api/v3) was retired and now returns HTTP 410 for every endpoint and version. Access is via the FTP/tabix distribution described at https://www.ebi.ac.uk/eqtl/Data_access/.

Examples

>>> import cellink as cl
>>> # cis-eQTLs at the BACH2 locus in OneK1K memory Tregs
>>> df = cl.resources.get_eqtl_catalog_dataset_associations(
...     "QTD000625", region="6:89900000-90300000"
... )
>>> df.nsmallest(5, "pvalue")[["rsid", "gene_id", "pvalue", "beta"]]