ThresholdClumpedRule

Threshold clumped variants rule

Description

ThresholdClumpedRule resolves one polygenius.model output for algorithm ClumpingThresholding.

Details

Reactive rule for the clumping+thresholding model output.

Execution logic:

  • requests GWAS input at required pval.max;

  • binds to clumped-variant resources after GWAS build is known;

  • applies the final pval threshold to clumped variants;

  • returns a PolyGeniusModel.

Super class

PolyGenius::Rule -> ThresholdClumpedRule

Methods

Public methods

Inherited methods

Method new()

Create the threshold-clumped rule.

Usage 
ThresholdClumpedRule$new()

Method matches()

Check whether this rule can produce the requested output.

Usage 
ThresholdClumpedRule$matches(output.spec)
Arguments
output.spec

Output resource specification.

Returns

TRUE for ClumpingThresholding model outputs.

Method inputs()

Build input specifications for this output.

Usage 
ThresholdClumpedRule$inputs(output.spec)
Arguments
output.spec

Output resource specification.

Returns

Named list with gwas and deferred clumped input.

Method bind()

Bind derived clumped input once GWAS build is known.

Usage 
ThresholdClumpedRule$bind(inputs, store, output.spec = NULL)
Arguments
inputs

Named list of input specifications.

store

Resource store.

output.spec

Output resource specification.

Returns

Updated named list of inputs.

Method requirements()

Declare resource requirements for this rule.

Usage 
ThresholdClumpedRule$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 clumping-thresholding model construction.

Usage 
ThresholdClumpedRule$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 
ThresholdClumpedRule$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.