RunLassosum2Rule

RunLassosum2Rule resolves lassosum2 polygenius.model outputs.

Reactive rule for model outputs generated by algorithm lassosum2.

The rule requests GWAS input at required pval.max, binds an ld.bigsnpr storage resource for the matched panel/build, matches GWAS variants to that storage in-process, runs lassosum2, and returns one dynamic model output for each candidate effect-size column returned by bigsnpr.

User-facing LD construction controls map onto ld.bigsnpr storage fields:

• ld.size -> window
• ld.thr -> threshold

These controls affect how the upstream bigsnpr LD storage is built. They are separate from native lassosum2 fitting arguments. Native fitting arguments are forwarded by name to bigsnpr::snp_lassosum2() when supported by the installed bigsnpr version. Missing arguments use the private function defaults, which mirror bigsnpr defaults.

The bigsnpr tutorial treats the returned lassosum2 matrix as a grid of candidate models and chooses among columns using prediction performance in a validation set. This rule does not receive validation genotypes or outcomes, so validation-set choice is left to downstream evaluation workflows.

PolyGenius::Rule -> RunLassosum2Rule

Public methods

• RunLassosum2Rule$new()
• RunLassosum2Rule$matches()
• RunLassosum2Rule$inputs()
• RunLassosum2Rule$bind()
• RunLassosum2Rule$requirements()
• RunLassosum2Rule$run()
• RunLassosum2Rule$clone()

Method new()

Create the lassosum2 rule.

Usage

RunLassosum2Rule$new()

Method matches()

Check whether this rule can produce the requested output.

Usage

RunLassosum2Rule$matches(output.spec)

Arguments

output.spec — Output resource specification.

Returns

TRUE for lassosum2 model outputs.

Method inputs()

Build input specifications for this output.

Usage

RunLassosum2Rule$inputs(output.spec)

Arguments

output.spec — Output resource specification.

Returns

Named list with required GWAS input and deferred LD input.

Method bind()

Bind LD storage input after GWAS build is known.

Usage

RunLassosum2Rule$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

RunLassosum2Rule$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 lassosum2 model construction.

Usage

RunLassosum2Rule$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.

Method clone()

The objects of this class are cloneable with this method.

Usage

RunLassosum2Rule$clone(deep = FALSE)

Arguments

deep — Whether to make a deep clone.

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