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

Ming Wai Yeung; Pim van der Harst; Niek Verweij

doi:10.1016/j.xpro.2022.101471

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

STAR Protoc. 2022 Jun 17;3(3):101471. doi: 10.1016/j.xpro.2022.101471. eCollection 2022 Sep 16.

Authors

Ming Wai Yeung¹, Pim van der Harst², Niek Verweij³

Affiliations

¹ University of Groningen, University Medical Center Groningen, Department of Cardiology, 9700 RB Groningen, the Netherlands; Department of Cardiology, Division of Heart & Lungs, University Medical Center Utrecht, University of Utrecht, Utrecht, the Netherlands. Electronic address: m.w.yeung@umcg.nl.
² University of Groningen, University Medical Center Groningen, Department of Cardiology, 9700 RB Groningen, the Netherlands; Department of Cardiology, Division of Heart & Lungs, University Medical Center Utrecht, University of Utrecht, Utrecht, the Netherlands.
³ University of Groningen, University Medical Center Groningen, Department of Cardiology, 9700 RB Groningen, the Netherlands. Electronic address: n.verweij@umcg.nl.

Abstract

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).

Keywords: Bioinformatics; Health Sciences; Systems biology.

MeSH terms

Biological Specimen Banks*
Humans
Information Storage and Retrieval*
Phenotype
United Kingdom

Abstract

MeSH terms

Grants and funding