RunPrscsRule

PRS-CS model rule

Description

RunPrscsRule resolves one polygenius.model output for PRS-CS.

Details

Reactive rule for model outputs generated by algorithm PRScs.

The rule requests GWAS input, binds an ld.prscs storage resource for the matched panel/build, writes neutral PRS-CS summary statistics and BIM inputs, runs the package Python wrapper, and converts posterior effects back into a PolyGeniusModel.

PRS-CS itself performs the GWAS/reference/validation intersection. The ld.prscs resource is therefore built on the full effective reference panel and not on a GWAS-specific subset.

Super class

PolyGenius::Rule -> RunPrscsRule

Methods

Public methods

• RunPrscsRule$new()

• RunPrscsRule$matches()

• RunPrscsRule$inputs()

• RunPrscsRule$bind()

• RunPrscsRule$requirements()

• RunPrscsRule$run()

• RunPrscsRule$clone()

Inherited methods

• PolyGenius::Rule$print()

---

Method new()

Create the PRS-CS rule.

Usage

RunPrscsRule$new()

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Method matches()

Check whether this rule can produce the requested output.

Usage

RunPrscsRule$matches(output.spec)

Arguments

output.spec

Output resource specification.

Returns

TRUE for PRScs model outputs.

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Method inputs()

Build input specifications for this output.

Usage

RunPrscsRule$inputs(output.spec)

Arguments

output.spec

Output resource specification.

Returns

Named list with gwas and deferred ld input.

---

Method bind()

Bind PRS-CS LD storage input after GWAS build is known.

Usage

RunPrscsRule$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

RunPrscsRule$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 PRS-CS model construction.

Usage

RunPrscsRule$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.

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Method clone()

The objects of this class are cloneable with this method.

Usage

RunPrscsRule$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.