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 explore the capabilities of the phenotype-services using the gorr package.

Load packages

First load the gorr package, the tidyverse package is recommended in general, but not required for this example

library(gorr)
library(magrittr) # pipe
library(tibble)

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 categories

All available categories can be listed by passing the conn object to the get_categories function

categories <- get_categories(conn)
categories

categories <- get_categories(conn)
tail(categories, 4)

The results come back as a vector of categories

Create category

If we want to add a new category to the catalog we can do so using create_category along with the name of the category to be added as follows.

NB: Before creating a new category, make sure you have the privileges (admin rights to category management) to do so.

name <- paste0("rtestcat", sample(1:99, 1)) # Name of new category
new_category <- create_category(name,  conn)

A new category has now been added and assigned to the variable new_category:

print(new_category)

Delete category

Categories can be removed from project by passing the name of the category to category_delete along with the connector object.

get_categories(conn)
print(name) # Category to be deleted
category_delete(name, conn)
get_categories(conn)

tail(get_categories(conn), 5)
print(name) # Category to be deleted
category_delete(name, conn)
tail(get_categories(conn), 4)

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