generate\(algorithm\)lassosum2

lassosum2 algorithm specification

Description

Configure a single lassosum2 algorithm specification.

Usage

`generate$algorithm$lassosum2`(reference.panel, pval = 1, delta = c(0.001, 0.01, 0.1, 1), lambda = NULL, ld.size = 3000, ld.thr = 0.002, ncores = 1)

Arguments

reference.panel

Character scalar reference-panel name used for LD.

variant.space

Optional variant-space name. When supplied, PolyGenius first creates a restricted reference panel from reference.panel and this variant space, then builds LD from that derived panel. Do not pass the name of an already restricted reference panel together with variant.space.

pval

Numeric scalar in ⁠[0, 1]⁠; GWAS p-value filter before fitting.

delta

Numeric sequence of lassosum2 delta values.

lambda

Optional numeric sequence of lassosum2 lambda values.

ld.size

Integer LD construction control mapped to bigsnpr window.

ld.thr

Numeric LD construction control mapped to bigsnpr threshold.

ncores

Integer worker cores to request for this algorithm.

Details

lassosum2 consumes the same ld.bigsnpr storage resource as LDpred2.

ld.size and ld.thr are lassosum2 workflow LD-construction controls and are mapped to bigsnpr LD storage fields:

  • ld.size -> window

  • ld.thr -> threshold

These are separate from lassosum2 fitting hyperparameters such as delta and lambda.

The current lassosum2 wrapper fixes the bigsnpr LD fields statistic = “r”, signed = TRUE, and phased = FALSE.

The bigsnpr lassosum2 tutorial treats the returned effect-size matrix as a grid of candidate models and chooses among them using prediction performance in a validation set. This generation declaration does not receive validation genotypes or outcomes, so tutorial-style validation-set model choice should be handled downstream when such data are available.

For lassosum2 parameter guidance, refer to the bigsnpr lassosum2 reference and extended polygenic-score documentation: https://privefl.github.io/bigsnpr/reference/snp_lassosum2.html and https://privefl.github.io/bigsnpr-extdoc/polygenic-scores-pgs.html.

Value

ResourceSpecSet of generate algorithm resources.