Covariate services

Andri M. Stefansson andri@genuitysci.com

2022-06-16

In this example, we’re going to demonstrate how to interact with the covariate services API using the gorr package.

Loading required packages

library(gorr)
library(magrittr) # pipe

Connect to Genuity Science’s services.

First we’ll need to establish a connection to our API services. To do that we’ll need to call platform_connect and provide it with the relevant parameters pointing to the phenotype-catalog-service, i.e. api_key and project:

conn <- platform_connect(api_key = Sys.getenv("GOR_API_KEY"),
                          project = Sys.getenv("GOR_API_PROJECT"))
conn
#> ── GOR API service connection ──────────────────────────────────────────────────
#> • Service Root/s: https://platform.wuxinextcodedev.com/api/query, https://platform.wuxinextcodedev.com/api/phenotype-catalog, https://platform.wuxinextcodedev.com/queryserver, https://platform.wuxinextcodedev.com/workflow
#> • Project: ukbb_hg38
#> • API key issued at: 2022-05-18 10:18:54
#> • API key expires at: Never
#> • Access token issued at: 2022-06-16 15:55:10
#> • Access token expires at: 2022-06-17 15:55:10

If everything goes as planned, we’ll have a conn object to pass into subsequent functions.

List available covariates

Covariates available to users can be listed by passing the conn object to get_covariates.

covariates <- get_covariates(conn)
covariates

The results come back as a list of covariates available to the user.

Get phenotype

Now can fetch a covariate from the project get_covariate and passing the covariate’s unique id along with the conn object .

covariate <- get_covariate(id = 1, conn)
covariate