generate\(algorithm\)PRScs
PRS-CS algorithm specification
Description
Configure a single PRS-CS algorithm specification.
Usage
`generate$algorithm$PRScs`(reference.panel, variant.space = NULL, pval = 1, phi = NULL, a = 1, b = 0.5, n.iter = 1000, n.burnin = 500, thin = 5, beta.std = FALSE, write.psi = FALSE, write.pst = FALSE, ld.block.size = 1000, python = NULL, seed = NULL, ncores = 1)
Arguments
reference.panel
|
Character scalar reference-panel name used for LD. |
variant.space
|
Optional variant-space name used to derive the effective reference panel before LD construction. |
pval
|
Numeric scalar in |
phi
|
Optional numeric global shrinkage parameter. |
a, b
|
Numeric PRS-CS prior parameters. |
n.iter, n.burnin, thin
|
Integer PRS-CS MCMC controls. |
beta.std
|
Logical; forwarded to PRS-CS. |
write.psi
|
Logical; forwarded to PRS-CS. |
write.pst
|
Logical; posterior-sample output is not converted into a PolyGenius model and is therefore currently unsupported for model generation. |
ld.block.size
|
Integer number of reference variants per PRS-CS LD block when PolyGenius builds neutral block files. |
python
|
Optional Python executable. When |
seed
|
Optional integer random seed. |
ncores
|
Integer worker cores to request for LD construction and the PRS-CS rule. |
Details
PRS-CS consumes ld.prscs storage built from the requested reference panel. When variant.space is supplied, PolyGenius first resolves a restricted reference panel and then builds PRS-CS LD blocks from that panel. The ld.prscs rule itself only receives the effective reference panel; it does not interpret the user-facing variant.space option.
PRS-CS fitting is delegated to the package Python wrapper, which expects the upstream PRS-CS Python modules to be importable in the selected Python environment.
Value
ResourceSpecSet of generate algorithm resources.