BuildLDBigsnprRule

Build bigsnpr LD storage rule

Description

Build bigsnpr LD storage rule

Build bigsnpr LD storage rule

Details

Reactive rule that materializes an ld.bigsnpr resource directly from a tidy reference.panel input using bigsnpr-native matrix operations.

This rule is the first-class producer for the bigsnpr-family LD storage used by LDpred2 and lassosum2. It converts the reference panel to a bigSNP object and computes LD with bigsnpr::snp_cor() chromosome-by-chromosome, avoiding the retired PLINK .vcor edge-table path entirely.

Before LD is computed, variants are filtered by minor allele frequency in the reference panel used to estimate LD. The threshold follows the LDpred2 tutorial convention, MAF > 1 / sqrt(n_reference_samples), to avoid unstable or undefined correlations for monomorphic and very rare variants in the LD reference sample.

Super class

PolyGenius::Rule -> BuildLDBigsnprRule

Methods

Public methods

• BuildLDBigsnprRule$new()

• BuildLDBigsnprRule$matches()

• BuildLDBigsnprRule$inputs()

• BuildLDBigsnprRule$requirements()

• BuildLDBigsnprRule$run()

• BuildLDBigsnprRule$clone()

Inherited methods

• PolyGenius::Rule$bind()
• PolyGenius::Rule$print()

---

Method new()

Create the bigsnpr LD storage rule.

Usage

BuildLDBigsnprRule$new()

---

Method matches()

Check whether this rule can produce the requested output.

Usage

BuildLDBigsnprRule$matches(output.spec)

Arguments

output.spec

Output resource specification.

Returns

TRUE for ld.bigsnpr outputs.

---

Method inputs()

Build required reference-panel input.

Usage

BuildLDBigsnprRule$inputs(output.spec)

Arguments

output.spec

Output resource specification.

Returns

Named list with the required reference.panel input.

---

Method requirements()

Declare resource requirements for this rule.

Usage

BuildLDBigsnprRule$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 bigsnpr LD materialization.

Usage

BuildLDBigsnprRule$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.

---

Method clone()

The objects of this class are cloneable with this method.

Usage

BuildLDBigsnprRule$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.