Package — Reference data

Reference download and path resolution (gl.download_ref, gl.get_path, …).

`download_ref`

Download a reference file based on its identifier from reference.json.

Parameters:

Name	Type	Description	Default
`name`	`str`	Reference file identifier	required

Returns:

Type	Description
`str or None`	Local path where the file was saved, or None if download failed

`get_path`

Retrieve the local file path for a specified reference file using keywords.

Returns the file path if found, otherwise False (or raises if raise_on_missing).

`check_format`

Check the header conversion dictionary between a given format and GWASLab format.

Parameters:

Name	Type	Description	Default
`fmt`	`str`	Format name to check	required
`log`	`Log`	Logger instance	required

Returns:

Type	Description
`Dict[str, str]`	Dictionary mapping format headers to GWASLab headers

`download_sumstats`

Download GWAS Catalog summary statistics for a given GCST accession.

Parameters:

Name	Type	Description	Default
`gcst_id`	`str`	GWAS Catalog study accession (e.g. "GCST90002446").	required
`output_dir`	`str`	Directory to store downloaded file. If None, uses the GWASLab default data directory from `options.paths["data_directory"]`. Files are then stored under `<output_dir>/<GCST_ID>/`.	required
`directory`	`str`	Alias for `output_dir`.	required
`filename`	`str`	Output filename. If None, defaults to "{GCST}_sumstats.tsv.gz".	required
`harmonised`	`bool`	If True, prioritize harmonised files. If harmonised files are not available, fall back to raw files. If False, select raw files directly (default: True).	required
`timeout`	`int`	HTTP request timeout in seconds (default: 60).	required
`chunk_size`	`int`	Download chunk size in bytes (default: 1MB).	required
`overwrite`	`bool`	Whether to overwrite existing output file (default: False).	required
`verbose`	`bool`	Whether to print log messages (default: True).	required
`log`	`Log`	Logger object. If None, a new logger is created.	required

Returns:

Type	Description
`str`	Absolute path of downloaded file.

Raises:

Type	Description
`ValueError`	`If GCST ID format is invalid.` RuntimeError If no downloadable summary statistics URL can be found. requests.exceptions.RequestException If the download request fails.

`get_power`

Calculate statistical power for genetic association studies.

Parameters:

Name	Type	Description	Default
`mode`	`(b, q)`	Calculation mode: - 'b' for binary traits (case-control) - 'q' for quantitative traits	`'b'`
`genotype_rr`	`float`	Genotype relative risk (GRR) for risk allele for binary traits	required
`genotype_or`	`float`	Genotype odds ratio (OR) for risk allele for binary traits	required
`beta`	`float`	Effect size (log scale) for quantitative traits	required
`eaf`	`float`	Effect allele frequency for quantitative traits	required
`n`	`int`	Total sample size for quantitative traits	required
`ncase`	`int`	Number of cases for binary mode	required
`ncontrol`	`int`	Number of controls for binary mode	required
`prevalence`	`float`	Disease prevalence in population	required
`or_to_rr`	`bool`	Convert OR to GRR using prevalence (Zhang & Kai method)	required
`daf`	`float`	Derived allele frequency	required
`sig_level`	`float`	Significance threshold (default: 5e-8)	required
`vary`	`float`	Phenotype variance for quantitative traits	required

Returns:

Type	Description
`float or array - like`	Calculated statistical power (0-1)

References

Skol, A. D., Scott, L. J., Abecasis, G. R., & Boehnke, M. (2006). 
Joint analysis is more efficient than replication-based analysis 
for two-stage genome-wide association studies. Nature genetics, 38(2), 209-213.

Zhang, J., & Kai, F. Y. (1998). What's the relative risk? 
A method of correcting the odds ratio in cohort studies of common outcomes. 
Jama, 280(19), 1690-1691.