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Software application profile: PHESANT: A tool for performing automated phenome scans in UK Biobank

Research output: Contribution to journalArticle

Original languageEnglish
Article numberdyx218
Pages (from-to)29-35
Number of pages7
JournalInternational Journal of Epidemiology
Volume47
Issue number1
Early online date6 Oct 2017
DOIs
DateAccepted/In press - 22 Aug 2017
DateE-pub ahead of print - 6 Oct 2017
DatePublished (current) - 1 Feb 2018

Abstract

Motivation: Epidemiological cohorts typically contain a diverse set of phenotypes such that automation of phenome scans is non-trivial, because they require highly heterogeneous models. For this reason, phenome scans have to date tended to use a smaller homogeneous set of phenotypes that can be analysed in a consistent fashion. We present PHESANT (PHEnome Scan ANalysis Tool), a software package for performing comprehensive phenome scans in UK Biobank. General features: PHESANT tests the association of a specified trait with all continuous, integer and categorical variables in UK Biobank, or a specified subset. PHESANT uses a novel rule-based algorithm to determine how to appropriately test each trait, then performs the analyses and produces plots and summary tables. Implementation: The PHESANT phenome scan is implemented in R. PHESANT includes a novel Javascript D3.js visualization and accompanying Java code that converts the phenome scan results to the required JavaScript Object Notation (JSON) format. Availability: PHESANT is available on GitHub at [https://github.com/MRCIEU/PHESANT]. Git tag v0.5 corresponds to the version presented here.

    Structured keywords

  • Jean Golding

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    Rights statement: This is the final published version of the article (version of record). It first appeared online via Oxford Academic at https://academic.oup.com/ije/article/doi/10.1093/ije/dyx204/4347232/Software-Application-Profile-PHESANT-a-tool-for . Please refer to any applicable terms of use of the publisher.

    Final published version, 395 KB, PDF-document

    Licence: CC BY

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