Phenotype categories

Andri M. Stefansson andri@genuitysci.com

2022-06-16

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
#> ── 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 15:55:55
#> • Access token expires at: 2022-06-17 15:55:55

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

#> [1] "statistics"     "cardiovascular" "rtestCat73"     "rtestCat16"

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)
#> $name
#> [1] "rtestcat47"

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)

#> [1] "statistics"     "cardiovascular" "rtestcat47"     "rtestCat73"    
#> [5] "rtestCat16"
#> [1] "rtestcat47"
#> Response [https://platform.wuxinextcodedev.com/api/phenotype-catalog/projects/ukbb_hg38/categories/rtestcat47]
#>   Date: 2022-06-16 15:55
#>   Status: 204
#>   Content-Type: <unknown>
#> <EMPTY BODY>
#> [1] "statistics"     "cardiovascular" "rtestCat73"     "rtestCat16"