| Title: | Software Application Profile: PHESANT: a tool for performing automated phenome scans in UK Biobank |
| Journal: | International Journal of Epidemiology |
| Published: | 5 Oct 2017 |
| Pubmed: | https://pubmed.ncbi.nlm.nih.gov/29040602/ |
| DOI: | https://doi.org/10.1093/ije/dyx204 |
| URL: | https://academic.oup.com/ije/article-pdf/47/1/29/25087820/dyx204.pdf |
| Citations: | 179 (55 in last 2 years) as of 8 Aug 2024 |
Publication 7534
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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.
5 Authors
- Louise AC Millard
- Neil M Davies
- Tom R Gaunt
- George Davey Smith
- Kate Tilling
Enabling scientific discoveries that improve human health