Utilities

Conversion helpers, coercions, chromosome recoding, and other supporting utilities.

as.bigsnpr	Converts a GenotypeInfo object to bigsnpr’s file-backed big.matrix format ( .rds + .bk files). This enables use of bigsnpr-based algorithms such as LDpred2 and lassosum2 while maintaining compatibility with PolyGenius workflows. Aliases: as.bigsnpr
as.list.ResourceSpecSet	Coerce a resource spec set to plain list Aliases: as.list.ResourceSpecSet
c.ResourceSpecSet	Concatenate resource spec sets Aliases: c.ResourceSpecSet
sub-.ResourceSpecSet	Subset a resource spec set Aliases: [.ResourceSpecSet
importPGSCatalogPRSs	importPGSCatalogPRSs() is a high-level adapter that imports one or more polygenic score (PGS) models from the PGS Catalog using the suggested package quincunx , and converts them into a PolyGeniusModelSet . Aliases: importPGSCatalogPRSs
liftover	This is a generic function that performs a liftover of variants between genome builds Aliases: liftover, liftover.PolyGeniusModelSet, liftover.PolyGeniusModel, liftover.data.frame, liftover.GenotypeInfo
recode_chromosome_codes	Re-encodes one or more chromosome columns according to the export formats supported in PLINK 2.0: https://www.cog-genomics.org/plink/2.0/data#export Aliases: recode_chromosome_codes
PolyGeniusAttribute	PolyGeniusAttribute() constructs a lightweight, list-based S3 object for arbitrary named metadata entries attached to PolyGenius objects. Aliases: PolyGeniusAttribute, print.PolyGeniusAttribute
slotAttributes	slotAttributes() and its replacement form &#8288;slotAttributes<-()&#8288; provide a generic S3 API for reading and writing grouped attribute payloads stored on PolyGenius objects. Aliases: slotAttributes, slotAttributes<-, slotAttributes.default, slotAttributes<-.default
slotArtifacts	slotArtifacts() and its replacement form &#8288;slotArtifacts<-()&#8288; provide a semantic wrapper around slotAttributes(x, “artifacts”) for plot-support payloads. Aliases: slotArtifacts, slotArtifacts<-, slotArtifacts.default, slotArtifacts<-.default
slotDiagnostics	slotDiagnostics() and its replacement form &#8288;slotDiagnostics<-()&#8288; provide a semantic wrapper around slotAttributes(x, “diagnostics”) for diagnostics payloads. Aliases: slotDiagnostics, slotDiagnostics<-, slotDiagnostics.default, slotDiagnostics<-.default
slotLog	slotLog() and its replacement form &#8288;slotLog<-()&#8288; provide a semantic wrapper around slotAttributes(x, “log”) for provenance and call-metadata payloads. Aliases: slotLog, slotLog<-, slotLog.default, slotLog<-.default
GenerateAlgorithmSpec	Generate algorithm specification Aliases: GenerateAlgorithmSpec