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

By Louise Amanda Claire Millard, Neil M Davies, Tom R Gaunt, George Davey Smith, Kate Tilling

Posted 26 Feb 2017
bioRxiv DOI: 10.1101/111500 (published DOI: 10.1093/ije/dyx204)

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 v0.2 corresponds to the version presented here.

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