EpiGraphDB is an analytical platform and database to support data mining in epidemiology. The platform incorporates a graph of causal estimates generated by systematically applying Mendelian randomization to a wide array of phenotypes, and augments this with a wealth of additional data from other bioinformatic sources. EpiGraphDB aims to support appropriate application and interpretation of causal inference in systematic automated analyses of many phenotypes.
epigraphdb is an R package to provide ease of access to EpiGraphDB services. We will refer to epigraphdb as the name of the R package whereas "EpiGraphDB" as the overall platform.
Installation
To install the latest development version from github ( devtools is required ):
# install.packages("devtools") devtools::install_github("MRCIEU/epigraphdb-r")
To install a stable version from CRAN:
install.packages("epigraphdb")
NOTE: while the package repository is “epigraphdb-r”, the R package name is “epigraphdb”.
Using epigraphdb
epigraphdb provides a simple and intuitive way to query the API, as:
library("epigraphdb") #> #> EpiGraphDB v0.3 (API: https://api.epigraphdb.org) #> mr(outcome_trait = "Body mass index") #> # A tibble: 370 x 12 #> exposure_id exposure_name outcome_id outcome_name estimate se #> <chr> <chr> <chr> <chr> <dbl> <dbl> #> 1 627 Epiandroster… 785 Body mass i… 0.0950 2.28e-3 #> 2 541 X-11787 835 Body mass i… -0.0578 1.77e-4 #> 3 971 Ulcerative c… 835 Body mass i… -0.0111 1.76e-4 #> 4 60 Waist circum… 835 Body mass i… 0.861 2.07e-2 #> 5 UKB-a:426 Eye problems… 94 Body mass i… -1.12 1.90e-2 #> 6 UKB-a:373 Ever depress… 95 Body mass i… -0.616 4.80e-4 #> 7 29 Birth length 95 Body mass i… -0.141 5.67e-4 #> 8 350 Laurate (12:… 974 Body mass i… 0.418 7.10e-3 #> 9 UKB-a:124 Treatment/me… 974 Body mass i… -5.14 1.08e-1 #> 10 95 Body mass in… 974 Body mass i… 0.981 2.79e-2 #> # … with 360 more rows, and 6 more variables: p <dbl>, ci_upp <dbl>, #> # ci_low <dbl>, selection <chr>, method <chr>, moescore <dbl>)
For more information on how to use the epigraphdb R package and how to use the API in R please check out the following articles:
Package functionalities
Users can use the general query function query_epigraphdb to get data from an API endpoint on EpiGraphDB without having to deal with HTTP requests by themselves. We also provide a list of functions (see the table below) that are equivalent to the upstream endpoints for the ease of use.
EpiGraphDB resources
| link | screenshot |
|---|---|
| docs |  |
| API |  |
| web application |  |
| r package |  |
Citation
Please cite EpiGraphDB as
Yi Liu, Benjamin Elsworth, Pau Erola, Valeriia Haberland, Gibran Hemani, Matt Lyon, Jie Zheng, Tom R Gaunt. 2020. EpiGraphDB: a database and data mining platform for health data science. bioRxiv. doi:10.1101/2020.08.01.230193.
@article {epigraphdb2020,
author = {Liu, Yi and Elsworth, Benjamin and Erola, Pau and Haberland, Valeriia and Hemani, Gibran and Lyon, Matt and Zheng, Jie and Gaunt, Tom R},
title = {{EpiGraphDB}: a database and data mining platform for health data science},
journal = {bioRxiv},
year = {2020},
doi = {10.1101/2020.08.01.230193},
url = {https://epigraphdb.org}
}
