Index

The ukbflow Book is the Quarto companion for the ukbflow R package.

The package website and API reference are generated by pkgdown. This book is a separate workspace for RAP-native UK Biobank workflows: setup notes, module walkthroughs, design context, examples, and review records.

Scope

This book focuses on practical analysis workflows rather than duplicating the function reference.

• prepare a RAP analysis environment;
• extract, decode, and derive UK Biobank phenotypes;
• build reproducible association and GRS workflows;
• produce publication-ready tables and figures;
• record module-level design decisions and maintenance notes.

Package Map

Area	Modules	Role
RAP setup	auth, fetch, extract, job	Authenticate to RAP, retrieve metadata and files, extract phenotype data, and monitor cloud jobs
Data preparation	decode, derive, ops	Decode UKB fields and values, derive analysis variables, check pipeline state, and manage cohort changes
Analysis	assoc, grs, plot	Run association models, compute genetic risk scores, and produce manuscript-ready outputs

How to Use

Start with the RAP setup chapters if you are preparing a new project. Move to data preparation once metadata and phenotype extraction are working. Use the analysis chapters as templates for survival, logistic, subgroup, GRS, and plotting workflows.

For full function documentation, use the ukbflow package site.