PolyGenius
Home
Guide
Scenarios
Advanced
Reference
Reference
Workspace
Home
Guide
Why PolyGenius
Minimal Mental Model
Model Generation and Evaluation
First End-to-End Analysis (Local, GRCh37)
GWAS Sources
Algorithms
Generation Patterns and Troubleshooting
Evaluate Models
Using Models on Cohorts
Working with PolyGeniusData
Compute in Depth
Association Analyses
Direct Regression Associations
Survival Associations
Stratification and Heterogeneity
Association Comparisons
Mediation
Mendelian Randomization
Meta-Analysis Of Associations
Visualization
Scenarios
Case study 1: Generating and prioritizing PGS models
Case study 2: Leveraging PGS models for downstream biological inference
Case study 3: Scalable multi-trait polygenic analysis with cross-cohort meta-analysis
Advanced
Data Architecture Deep Dive
Execution Engine Caching and Registries
PolyGenius Execution Engine
Extending PolyGenius
Code Organization and Contribution
API Quick Reference
Glossary, FAQ, and Reporting Checklist
Reference
Generate
generate
generate$models
Sources
generate$sources$local
generate$sources$gwascatalog
generate$sources$opengwas
Algorithms
generate$algorithm$ClumpingThresholding
generate$algorithm$LDpred2
generate$algorithm$lassosum2
generate$algorithm$PRScs
generate$algorithm$COJO
Evaluate
evaluate
evaluate$benchmark
evaluate$discrimination
evaluate$calibration
evaluate$incremental
evaluate$compare
evaluate$similarity
evaluate$risk.strata
Compute
compute
compute$scores
compute$population.structure
compute$kinship
compute$single.variant.associations
compute$similarity$obs
compute$embedding$obs
Associate
associate
Workflows
associate$regression
associate$mediation
associate$mr
associate$meta
associate$compare
Regression Families
LinearRegression
LogisticRegression
CoxRegression
CompetingRiskRegression
KaplanMeierRegression
Association Schemas
schemaLm
schemaGlm
schemaKm
schemaCox
schemaCrr
schemaMediation
associate.schema.comparison
associate.schema.mediation
associate.schema.meta
associate.schema.mr
Comparison Families
LinearComparison
LogisticComparison
CoxComparison
CompetingRiskComparison
KaplanMeierComparison
Visualize
visualize
Data
Scores
visualize$data$scores$distribution
visualize$data$scores$distribution.heatmap
visualize$data$scores$heatmap
Similarity and Embedding
visualize$data$similarity
Associations
visualize$associations$heatmap
visualize$associations$forest
visualize$associations$survival
Evaluation
Overview
visualize$evaluate$leaderboard
visualize$evaluate$overview$metric.heatmap
Discrimination
visualize$evaluate$discrimination$curve
visualize$evaluate$discrimination$roc
visualize$evaluate$discrimination$pr
visualize$evaluate$discrimination$confusion
visualize$evaluate$discrimination$distribution
visualize$evaluate$discrimination$predicted.vs.observed
visualize$evaluate$discrimination$residuals
visualize$evaluate$discrimination$forest
Calibration
visualize$evaluate$calibration$curve
visualize$evaluate$calibration$slope.intercept
Comparison and Incremental Value
visualize$evaluate$compare$delta.forest
visualize$evaluate$compare$delta.heatmap
visualize$evaluate$incremental$delta
Similarity and Risk Strata
visualize$evaluate$similarity$heatmap
visualize$evaluate$risk.strata$profile
visualize$evaluate$risk.strata$lift
Diagnostics
visualize$evaluate$diagnostics$metric.flags
Workspace
workspace
Catalogs
workspace$catalogs$genomeBuilds
workspace$catalogs$referencePanels
workspace$catalogs$variantSpaces
workspace$catalogs$liftoverChains
workspace$catalogs$LDs
workspace$catalogs$plink
Data Classes
Models
PolyGeniusModel
PolyGeniusModelSet
Cohorts and Results
PolyGeniusData
PolyGeniusAssociations
PolyGeniusEvaluation
PolyGeniusFrame
PolyGeniusFrameSet
roles
Genotypes
GenotypeInfo
GenotypeInfoSet
GenotypeInfoSet-class
Core and Execution
User Interfaces
execute
Runtime and Options
PolyGeniusLogAttribute
Engines
ExecutionEngine
GenerateModelsEngine
Resources and Rules
Resource Specifications
ResourceSpec
ResourceSpecSet
Rule Infrastructure
Rule
RuleRegistry
resources.factory
resources.type
catalogs-reference-panels-rules
catalogs-variant-spaces-rules
catalogs-liftover-chains-rules
rules.liftover.chains
rules.algorithms
rules.sources
Algorithm Rules
ClumpVariantsRule
BuildLDBigsnprRule
RunLdPred2Rule
RunLassosum2Rule
RunCojoRule
BuildLDPrscsRule
RunPrscsRule
ThresholdClumpedRule
Source Rules
FetchGWASCatalogRule
FetchOpenGWASRule
LoadLocalGWASRule
Reference Panel Rules
ConvertReferencePanelRule
DownloadReferencePanelRule
LiftoverReferencePanelRule
RestrictReferencePanelRule
Liftover Chain Rules
DownloadLiftoverChainRule
Utilities
as.bigsnpr
as.list.ResourceSpecSet
c.ResourceSpecSet
sub-.ResourceSpecSet
importPGSCatalogPRSs
liftover
recode_chromosome_codes
PolyGeniusAttribute
slotAttributes
slotArtifacts
slotDiagnostics
slotLog
GenerateAlgorithmSpec
Reference
Workspace
Workspace
Runtime configuration, workspace catalogs, and user-level resource inventories.
workspace
The active workspace owns runtime configuration, catalogs, and advanced internals used by generate , compute , evaluate , associate , and visualize .
Aliases:
workspace
Catalogs
Workspace catalog registries for genome resources and local executables.
6 child items
visualize$evaluate$diagnostics$metric.flags
workspace