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Publication - Dr Tom Gaunt

    PHESANT

    a tool for performing automated phenome scans in UK Biobank

    Citation

    Millard, L, Davies, N, Gaunt, T, Smith, GD & Tilling, K, 2017, ‘PHESANT: a tool for performing automated phenome scans in UK Biobank’. International Journal of Epidemiology.

    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.

    Full details in the University publications repository