ClumpVariantsRule

Clump variants rule

Description

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

Details

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.

Super class

PolyGenius::Rule -> ClumpVariantsRule

Methods

Public methods

Inherited methods

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)
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.