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Populations, Samples and Linkage Disequilibrium: parameters and notes

See the tutorial for usage and examples.

Each function includes its purpose, API, inputs, outputs, example code and result description. Prepare any required credentials, local files and optional dependencies; remote results vary with database releases and query time.

List IGSR and 1000 Genomes data collections

dnakit.databases.igsr_list_data_collections(*, operation=None, limit=None, verbose=True)

Parameter Type Required / default Description and constraints
operation string None Operation type (fixed: list_data_collections).
limit integer None Maximum number of results to return.
verbose bool True Progress flag.

Search 1000 Genomes populations

dnakit.databases.igsr_search_populations(*, operation=None, superpopulation=None, query=None, limit=None, verbose=True)

Parameter Type Required / default Description and constraints
operation string None Operation type (fixed: search_populations).
superpopulation string | null None Filter by superpopulation code: AFR (African), AMR (Admixed American), EAS (East Asian), EUR (European), SAS (South Asian). Leave empty for all.
query string | null None Free-text search query to find populations by name or description (e.g., 'Chinese', 'Yoruba', 'British').
limit integer None Maximum number of results to return.
verbose bool True Progress flag.

Search 1000 Genomes samples by population or collection

dnakit.databases.igsr_search_samples(*, operation=None, population=None, data_collection=None, sample_name=None, limit=None, verbose=True)

Parameter Type Required / default Description and constraints
operation string None Operation type (fixed: search_samples).
population string | null None Filter by population code (e.g., 'CHB', 'YRI', 'GBR', 'CEU'). Use IGSR_search_populations to find valid codes.
data_collection string | null None Filter by data collection title (e.g., '1000 Genomes 30x on GRCh38', '1000 Genomes on GRCh38').
sample_name string | null None Look up specific sample by name (e.g., 'HG00096', 'NA12878').
limit integer None Maximum number of results to return.
verbose bool True Progress flag.

dnakit.databases.ldlink_get_proxies(*, variant, population=None, r2_threshold=None, genome_build=None, limit=None, verbose=True)

Parameter Type Required / default Description and constraints
variant string Required Query SNP rsID, e.g. 'rs7903146'.
population string | null None 1000 Genomes population code (default 'CEU'). Examples: 'CEU' (European), 'YRI' (African), 'CHB' (East Asian), or super-populations 'EUR'/'AFR'/'EAS'/'SAS'/'AMR'.
r2_threshold number | null None Minimum R2 to report (default 0.8; high LD).
genome_build string | null None 'grch38' (default) or 'grch37'.
limit integer | null None Max proxies to return (1-500, default 50).
verbose bool True Progress flag.