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 run a simple remote gor query 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)

Connecting to the direct query service

First we'll need to establish a connection to our direct query API. To do that we'll need to call gor_connect and provide it with the relevant parameters pointing to the direct-query-service, i.e. api_key and project:

api_key <- Sys.getenv("GOR_API_KEY")
conn <- gor_connect(api_key, project = Sys.getenv("GOR_API_PROJECT"))
conn

If everything goes as planned, we'll have a conn object to pass into the gor_query function to finally run a query:

result <- gor_query("gor #dbsnp# | top 100", conn)

The results come back as an R data.frame:

print(result)

It should also be noted that larger gor queries can be constructed inside a string block and piped directly into the gor_query function:

chr21_results <- "
  gor -p chr21 #dbsnp# 
    | where len(reference)=1 and len(allele)=1
    | calc snptype reference+'/'+allele 
    | hide rsIDs
    | top 100" %>%
    gor_query(conn)