ClumpVariantsRule

ClumpVariantsRule resolves one clumped.variants output by loading a GWAS resource and a matching reference panel, then running panel clumping.

Reactive rule that builds clumped.variants from GWAS summary statistics and a reference panel.

Execution logic:

• requires a resolved reference panel build;
• loads GWAS summary statistics and panel (pfile);
• optionally filters variants by eaf.threshold;
• runs panel clumping and returns clumped variants plus metadata.

PolyGenius::Rule -> ClumpVariantsRule

Public methods

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

Method new()

Create the clump variants rule.

Usage

ClumpVariantsRule$new()

Method matches()

Check whether this rule can produce the requested output.

Usage

ClumpVariantsRule$matches(output.spec)

Arguments

output.spec — Output resource specification.

Returns

TRUE for clumped.variants outputs.

Method inputs()

Build input specifications for clumping.

Usage

ClumpVariantsRule$inputs(output.spec)

Arguments

output.spec — Output resource specification.

Returns

Named list with gwas and panel inputs.

Method requirements()

Declare resource requirements for this rule.

Usage

ClumpVariantsRule$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 variant clumping.

Usage

ClumpVariantsRule$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

ClumpVariantsRule$clone(deep = FALSE)

Arguments

deep — Whether to make a deep clone.

Other algorithm-rules: BuildLDBigsnprRule, BuildLDBlocksRule, RunLassosum2Rule, RunLdPred2Rule, RunPrscsRule, ThresholdClumpedRule