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

Ming Wai Yeung
, Pim van der Harst
, Niek Verweij

Research output: Contribution to journal › Article › Academic › peer-review

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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).

Original language	English
Article number	101471
Journal	STAR protocols
Volume	3
Issue number	3
DOIs	https://doi.org/10.1016/j.xpro.2022.101471
Publication status	Published - 16 Sept 2022

Keywords

Bioinformatics
Health Sciences
Systems biology

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10.1016/j.xpro.2022.101471Licence: CC BY

1-s2.0-S2666166722003513-mainFinal published version, 5.03 MBLicence: CC BY

Cite this

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

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",

author = "Yeung, \{Ming Wai\} and \{van der Harst\}, Pim and Niek Verweij",

note = "Funding Information: This research has been conducted using the UK Biobank resource under application number 74395. We thank all UK Biobank participants for their contributions. M.W.Y. and N.V. conceptualized and developed the ukbpheno package and the protocols. M.W.Y. performed the analyses and wrote the manuscript. N.V. and P.v.d.H. reviewed and edited the manuscript. P.v.d.H. provided the data and project administration. N.V. is a full-time employee of Regeneron Pharmaceutical Inc. and receives stock options and restricted stock units as compensation. Publisher Copyright: {\textcopyright} 2022 The Author(s)",

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doi = "10.1016/j.xpro.2022.101471",

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AU - van der Harst, Pim

AU - Verweij, Niek

N1 - Funding Information: This research has been conducted using the UK Biobank resource under application number 74395. We thank all UK Biobank participants for their contributions. M.W.Y. and N.V. conceptualized and developed the ukbpheno package and the protocols. M.W.Y. performed the analyses and wrote the manuscript. N.V. and P.v.d.H. reviewed and edited the manuscript. P.v.d.H. provided the data and project administration. N.V. is a full-time employee of Regeneron Pharmaceutical Inc. and receives stock options and restricted stock units as compensation. Publisher Copyright: © 2022 The Author(s)

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N2 - 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).

AB - 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).

KW - Bioinformatics

KW - Health Sciences

KW - Systems biology

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

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