In wuxi-nextcode/gorr: Genuity Science service API for R

requireNamespace("knitr")
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

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

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

wuxi-nextcode/gorr documentation built on Jan. 1, 2023, 7:54 a.m.