SetupBigsnprRule

Reactive rule for the R package dependencies required by the LDpred2, lassosum2, and bigsnpr LD algorithms. SetupBigsnprRule installs bigsnpr, bigsparser, and RhpcBLASctl into the active R library if they are absent. BuildLDBigsnprRule declares this rule as an input so the install runs before any LD matrix build is attempted.

bigsnpr setup rule

PolyGenius::Rule -> SetupBigsnprRule

Public methods

• SetupBigsnprRule$new()
• SetupBigsnprRule$matches()
• SetupBigsnprRule$inputs()
• SetupBigsnprRule$requirements()
• SetupBigsnprRule$run()

Method new()

Create the rule.

Usage

SetupBigsnprRule$new()

Method matches()

Check whether this rule produces the requested output.

Usage

SetupBigsnprRule$matches(output.spec)

Arguments

output.spec — Output resource specification.

Returns

TRUE for a bigsnpr output.

Method inputs()

Declare upstream inputs.

Usage

SetupBigsnprRule$inputs(output.spec)

Arguments

output.spec — Output resource specification.

Returns

An empty list; the rule has no inputs.

Method requirements()

Declare resource requirements.

Usage

SetupBigsnprRule$requirements(output.spec, inputs)

Arguments

output.spec — Output resource specification.

inputs — Bound input values.

Returns

Named list with cores and memory.

Method run()

Resolve the resource.

Usage

SetupBigsnprRule$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.

Rule, BuildLDBigsnprRule

Other setup-rules: ResolveGctbRule, ResolvePlinkRule, SetupLiftoverRule, SetupPrscsRule