LoadLocalGWASRule

LoadLocalGWASRule resolves a local GWAS request into one gwas.sumstats resource.

Reactive rule that materializes gwas.sumstats resources from local GWAS data provided in request metadata.

Execution logic:

• reads gwas, metadata, and pval.max from request metadata;
• evaluates gwas when provided as a function;
• drops variants with no usable coordinate and records the count;
• validates presence and wraps data in PGS;
• returns normalized metadata for cache/index tracking.

PolyGenius::Rule -> LoadLocalGWASRule

Public methods

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

Method new()

Create the local GWAS load rule.

Usage

LoadLocalGWASRule$new()

Method matches()

Check whether this rule can produce the requested output.

Usage

LoadLocalGWASRule$matches(output.spec)

Arguments

output.spec — Output resource specification.

Returns

TRUE for local gwas.sumstats outputs.

Method inputs()

Build rule input specifications.

Usage

LoadLocalGWASRule$inputs(output.spec)

Arguments

output.spec — Output resource specification.

Returns

Empty named list; local source details live on output.spec.

Method requirements()

Declare resource requirements for this rule.

Usage

LoadLocalGWASRule$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 local GWAS materialization for one request.

Usage

LoadLocalGWASRule$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

LoadLocalGWASRule$clone(deep = FALSE)

Arguments

deep — Whether to make a deep clone.

Other source-rules: FetchGWASCatalogRule, FetchOpenGWASRule, FetchPGSCatalogRule