EpiGraphDB • epigraphdb

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`