FetchGWASCatalogRule

FetchGWASCatalogRule resolves a single GWAS Catalog request into one gwas.sumstats resource.

Reactive rule that materializes gwas.sumstats resources from GWAS Catalog requests.

Retrieval is arranged as a ladder so that anything reachable on the GWAS Catalog is reachable here, regardless of how a study is exposed through the REST API:

• the harmonized FTP directory is derived deterministically from the accession (blocks of 1000), so no study-metadata endpoint is required to locate the data -- this is the primary path;
• harmonized metadata (YAML) and summary statistics are read from that directory, trying the conventional file names first and falling back to a directory listing for legacy layouts;
• study-level metadata is fetched as optional enrichment (REST v2, then v1); any failure is swallowed and never blocks retrieval;
• all sources are folded into one canonical metadata bag in which trait and build are always populated (harmonized YAML is the reliable floor);
• summary statistics are read column-selected and filtered at pval <= pval.max before any per-column coercion;
• beta is taken from the reported effect size where a row has one and derived as log(odds_ratio) where it does not. The fallback is per row, not per column: a harmonized file carries both columns whatever the study reported, so a study that published odds ratios leaves the beta column present and empty. The fetch fails only when no row has a usable value in either.

beta and se are on the log scale in what this rule emits; odds_ratio, ci_lower and ci_upper are passed through on the ratio scale as the Catalog published them. Nothing in PolyGenius reads the latter three, but anyone inspecting $variants directly should know the table holds both.

PolyGenius::Rule -> FetchGWASCatalogRule

Public methods

• FetchGWASCatalogRule$new()
• FetchGWASCatalogRule$matches()
• FetchGWASCatalogRule$inputs()
• FetchGWASCatalogRule$requirements()
• FetchGWASCatalogRule$run()
• FetchGWASCatalogRule$clone()

Method new()

Create the GWAS Catalog fetch rule.

Usage

FetchGWASCatalogRule$new()

Method matches()

Check whether this rule can produce the requested output.

Usage

FetchGWASCatalogRule$matches(output.spec)

Arguments

output.spec — Output resource specification.

Returns

TRUE for GWAS Catalog gwas.sumstats outputs.

Method inputs()

Build rule input specifications.

Usage

FetchGWASCatalogRule$inputs(output.spec)

Arguments

output.spec — Output resource specification.

Returns

Empty named list; GWAS Catalog source details live on output.spec.

Method requirements()

Declare resource requirements for this rule.

Usage

FetchGWASCatalogRule$requirements(output.spec, inputs)

Arguments

output.spec — Output resource specification.

inputs — Bound input values/specifications.

Returns

Named list with cores and memory.

Method run()

Execute GWAS Catalog retrieval for one request.

Usage

FetchGWASCatalogRule$run(output.spec, inputs, logger = pg.logger())

Arguments

output.spec — Output resource specification.

inputs — Named list of bound input values.

logger — Rule logger.

Returns

Rule result list with data, meta, and logs.

Method clone()

The objects of this class are cloneable with this method.

Usage

FetchGWASCatalogRule$clone(deep = FALSE)

Arguments

deep — Whether to make a deep clone.

Other source-rules: FetchOpenGWASRule, FetchPGSCatalogRule, LoadLocalGWASRule