BuildLDPrscsRule

Build PRS-CS LD block storage rule

Description

Build PRS-CS LD block storage rule

Build PRS-CS LD block storage rule

Details

Reactive rule that materializes an ld.prscs resource from a tidy bfile reference.panel.

The rule builds the neutral PolyGenius PRS-CS reference layout:

  • snpinfo

  • ⁠ldblk_chr<chrom>.hdf5⁠

The snpinfo file uses the columns consumed by PRS-CS (CHR, SNP, BP, A1, A2, MAF) without embedding any HM3, 1KG, or UKBB naming assumption. HDF5 chromosome files contain ⁠blk_<n>⁠ groups with ldblk and snplist datasets, matching the structure consumed by PRS-CS.

This rule receives an already resolved reference panel. User-facing variant.space selection is handled by algorithm binding before this rule is requested.

Super class

PolyGenius::Rule -> BuildLDPrscsRule

Methods

Public methods

Inherited methods

Method new()

Create the PRS-CS LD storage rule.

Usage 
BuildLDPrscsRule$new()

Method matches()

Check whether this rule can produce the requested output.

Usage 
BuildLDPrscsRule$matches(output.spec)
Arguments
output.spec

Output resource specification.

Returns

TRUE for ld.prscs outputs.

Method inputs()

Build required reference-panel input.

Usage 
BuildLDPrscsRule$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 
BuildLDPrscsRule$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 LD block materialization.

Usage 
BuildLDPrscsRule$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 
BuildLDPrscsRule$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.