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Publication - Dr Tom Gaunt

    Software application profile

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

    Citation

    Millard, LA, Davies, NM, Gaunt, TR, Smith, GD & Tilling, K, 2018, ‘Software application profile: PHESANT: A tool for performing automated phenome scans in UK Biobank’. International Journal of Epidemiology, vol 47., pp. 29-35

    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.

    Full details in the University publications repository