ThresholdClumpedRule

ThresholdClumpedRule resolves one polygenius.model output for algorithm ClumpingThresholding.

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 PGS.

PolyGenius::Rule -> ThresholdClumpedRule

Public methods

• ThresholdClumpedRule$new()
• ThresholdClumpedRule$matches()
• ThresholdClumpedRule$inputs()
• ThresholdClumpedRule$bind()
• ThresholdClumpedRule$requirements()
• ThresholdClumpedRule$run()
• ThresholdClumpedRule$clone()

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 = 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

ThresholdClumpedRule$clone(deep = FALSE)

Arguments

deep — Whether to make a deep clone.

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