The PEACOK R package implementation focuses on separating phenotype matrix generation from statistical association tests. It also allows statistical tests to be performed separately on different computing environments, such as on a high-performance computing cluster or an AWS Batch environment. This package introduces additional functionalities, including the ability to generate phenotypes for every node from a tree-like UKB data code (for example, an ICD-10 code) and to run logistic regression on a binary phenotype with covariates. Various downstream analysis and summarization were performed using R v3.4.3 https://cran.r-project.org. R libraries data.table (v1.12.8; https://CRAN.R-project.org/package=data.table), MASS (7.3-51.6; https://www.stats.ox.ac.uk/pub/MASS4/), tidyr (1.1.0; https://CRAN.R-project.org/package=tidyr) and dplyr (1.0.0; https://CRAN.R-project.org/package=dplyr) were also used.
