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- Title
Software Application Profile: PHESANT: a tool for performing automated phenome scans in UK Biobank.
- Authors
Millard, Louise AC; Davies, Neil M; Gaunt, Tom R; Smith, George Davey; Tilling, Kate; Millard, Louise A C; Davey Smith, George
- Abstract
<bold>Motivation: </bold>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.<bold>General features: </bold>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.<bold>Implementation: </bold>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.<bold>Availability: </bold>PHESANT is available on GitHub at [https://github.com/MRCIEU/PHESANT]. Git tag v0.5 corresponds to the version presented here.
- Subjects
COMPUTER software; EPIDEMIOLOGY; COHORT analysis; PHENOTYPES; ALGORITHMS; JSON (Document markup language)
- Publication
International Journal of Epidemiology, 2018, Vol 47, Issue 1, p29
- ISSN
0300-5771
- Publication type
journal article
- DOI
10.1093/ije/dyx204