ukbpheno v1.0: An R package for phenotyping health-related outcomes in the UK Biobank

The complexity and volume of data associated with population-based cohorts means that generating health-related outcomes can be challenging. Using one such cohort, the UK Biobank-a major open access resource-we present a protocol to efficiently integrate the main dataset and record-level data files, to harmonize and process the data using an R package named ukbpheno. We describe how to use the package to generate binary phenotypes in a standardized and machine-actionable manner. For complete details on the use and execution of this protocol, please refer to Yeung et al. (2022).

Automated summary

This article presents a protocol for efficiently integrating and processing complex data from population-based cohorts using the UK Biobank and the R package ukbpheno. The protocol allows for the generation of standardized and machine-actionable binary phenotypes.