FetchGWASCatalogRule

GWAS Catalog fetch rule

Description

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

Details

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

Execution logic:

  • reads pval.max from request metadata;

  • fetches base study metadata from the GWAS Catalog REST API;

  • resolves the harmonized directory from full_summary_stats;

  • fetches harmonized metadata YAML and harmonized sumstats;

  • maps harmonized/raw source columns into PolyGenius standard fields;

  • filters variants at pval <= pval.max;

  • wraps returned data and metadata for cache persistence.

Super class

PolyGenius::Rule -> FetchGWASCatalogRule

Methods

Public methods

Inherited methods

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

Named list with one gwas.request input.

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)
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.