Millard Louise A C, Davies Neil M, Gaunt Tom R, Davey Smith George, Tilling Kate
MRC Integrative Epidemiology Unit (IEU), School of Social and Community Medicine.
Intelligent Systems Laboratory, Department of Computer Science, University of Bristol, Bristol, UK.
Int J Epidemiol. 2018 Feb;47(1):29-35. doi: 10.1093/ije/dyx204. Epub 2017 Oct 5.
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.
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.
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.
PHESANT is available on GitHub at [https://github.com/MRCIEU/PHESANT]. Git tag v0.5 corresponds to the version presented here.
流行病学队列通常包含各种各样的表型，因此全表型扫描的自动化并非易事，因为它们需要高度异质的模型。因此，迄今为止，全表型扫描倾向于使用一组较小的、可采用一致方式进行分析的同质表型。我们展示了PHESANT（全表型扫描分析工具），这是一个用于在英国生物银行中进行全面全表型扫描的软件包。
PHESANT测试指定性状与英国生物银行中的所有连续、整数和分类变量或指定子集之间的关联。PHESANT使用一种新颖的基于规则的算法来确定如何适当地测试每个性状，然后进行分析并生成图表和汇总表。
PHESANT全表型扫描是在R语言中实现的。PHESANT包括一个新颖的Javascript D3.js可视化以及将全表型扫描结果转换为所需的JavaScript对象表示法（JSON）格式的配套Java代码。
PHESANT可在GitHub上获取，网址为[https://github.com/MRCIEU/PHESANT]。Git标签v0.5对应此处展示的版本。
