cellink.resources.get_1000genomes_ld_scores

cellink.resources.get_1000genomes_ld_scores(config_path='./cellink/resources/config/1000genomes.yaml', population='EUR', data_home=None, return_path=False, refresh=False, gwas_ancestry=None, on_ancestry_mismatch='warn')

Download, extract, and load precomputed 1000 Genomes linkage disequilibrium (LD) scores.

This function downloads population-specific LD scores from the 1000 Genomes project, extracts them to a local directory, and concatenates chromosome-wise annotation and LD score files into pandas DataFrames.

Parameters:

• config_path (str or pathlib.Path, default='./cellink/resources/config/1000genomes.yaml') – Path to YAML configuration file specifying URLs and file names for LD scores.

• population (str, default='EUR') – Population code for LD scores. Must be one of {‘EUR’, ‘EAS’}.

• data_home (str or pathlib.Path, optional) – Root directory where data will be stored. Defaults to user-specific cache directory.

• return_path (bool, default=False) – If True, returns the path to the extracted files and file prefix instead of DataFrames.

• refresh (bool, default=False) – If True, re-downloads and re-extracts files even if they already exist locally.

• gwas_ancestry (str or list of str, optional) – The GWAS’s own declared sample ancestry (e.g. from a GWAS Catalog study’s samples[].sample_ancestry_category). If given, warns (or raises, per on_ancestry_mismatch) when it doesn’t plausibly match population, see check_ancestry_match().

• on_ancestry_mismatch (str, default="warn") – "warn" | "error" | "ignore", forwarded to check_ancestry_match().

Return type:

tuple[DataFrame, DataFrame, str] | tuple[Path, str]

Returns:

tuple If return_path=False, returns (annot, ldscores, prefix): - annot : pd.DataFrame

Concatenated annotation files for all chromosomes.

• ldscorespd.DataFrame

  Concatenated LD score files for all chromosomes.

• prefixstr

  File name prefix used in the extracted data.

If return_path=True, returns (DATA, prefix): - DATA : pathlib.Path

Path to the directory containing extracted files.

• prefixstr

  File name prefix used in the extracted data.

Raises:

ValueError – If population is not one of the populations listed in the configuration.