generate\(algorithm\)ClumpingThresholding

Clumping and Thresholding (C+T) algorithm specification

Description

Construct clumping + p-value thresholding (C+T) algorithm specifications used by the reactive generate engine. When multiple thresholds are provided, the model output specifications are expanded to one per threshold.

Usage

`generate$algorithm$ClumpingThresholding`(pval, reference.panel, eaf.threshold = 0, clump.p1 = 1e-4, clump.r2 = 0.5, clump.kb = 250)

Arguments

pval	Numeric scalar or vector.
reference.panel	Character scalar reference-panel name.
variant.space	Optional variant-space name. When supplied, PolyGenius first creates a restricted reference panel from reference.panel and this variant space, then uses that derived panel for clumping. Do not pass the name of an already restricted reference panel together with variant.space.
eaf.threshold	Numeric effect-allele-frequency filter.
clump.p1	Numeric clumping p-value threshold.
clump.r2	Numeric clumping r^2 threshold.
clump.kb	Numeric clumping window in kilobases.

Value

ResourceSpecSet of generate algorithm resources.