Skip to content
R package for epigraphdb
R Makefile CSS
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
.github
R
inst
man
pkgdown
tests Add query_epigraphdb Dec 2, 2019
vignettes
.Rbuildignore
.gitignore
.lintr
.travis.yml
DESCRIPTION
LICENSE.md
Makefile
NAMESPACE
NEWS.md
README.md
_pkgdown.yml
codecov.yml
cran-comments.md
epigraphdb.Rproj

README.md

EpiGraphDB R package epigraphdb

CRAN status Travis build status Codecov test coverage

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

devtools is required to install from github:

# install.packages("devtools")
devtools::install_github("MRCIEU/epigraphdb-r")

NOTE: while the package repository is "epigraphdb-r", the R package name is "epigraphdb".

Using epigraphdb

library("epigraphdb")
#>   EpiGraphDB v0.2
#>
#>   Web API: http://api.epigraphdb.org
#>
#>   To turn off this message, use
#>   suppressPackageStartupMessages({library("epigraphdb")})
mr(outcome = "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>)

Functionalities

Below is a list of functionalities that are supported by the epigraphdb package. Advanced users are encouraged to use the API service directly.

API r package
General query
query_epigraphdb
Topic queries
GET /mr mr
GET /ontology ontology
GET /obs_cor obs_cor
GET /gwas_cor gwas_cor
GET /pqtl/ pqtl
GET /pqtl/pleio/ pqtl_pleio
GET /pqtl/list pqtl_list
GET /confounder confounder
GET /pathway pathway
GET /drugs/risk-factors drugs_risk_factors
GET /xqtl/multi-snp-mr xqtl_multi_snp_mr
GET /xqtl/single-snp-mr xqtl_single_snp_mr
GET /literature/mr literature_mr
Metadata
GET /meta/schema
GET /meta/nodes/list
GET /meta/nodes/{meta_node}/list
GET /meta/nodes/{meta_node}/list-names
GET /meta/nodes/{meta_node}/search
GET /meta/nodes/{meta_node}/search-neighbour
GET /meta/rels/list
GET /meta/rels/{meta_rel}/list

EpiGraphDB resources

link screenshot
docs docs
API api
web application webapp
r package epigraphdb-r

Citation

If Using EpiGraphDB or the epigraphdb R package:

Liu Y, Elsworth B, Haberland V, Erola P, Lyon M, Zheng J, Gaunt TR. EpiGraphDB: a database and data mining platform for health data science.

You can’t perform that action at this time.