inst/scripts/OpenTargets.R

In gaawr2: Genetic Association Analysis

run_OpenTargets <- function()
{
  library(httr)
  library(jsonlite)
  library(knitr)
  library(kableExtra)

  gene_id <- "ENSG00000164308"
  query_string = "
    query target($ensemblId: String!){
      target(ensemblId: $ensemblId){
        id
        approvedSymbol
        biotype
        geneticConstraint {
          constraintType
          exp
          obs
          score
          oe
          oeLower
          oeUpper
        }
        tractability {
          label
          modality
          value
        }
      }
    }
  "
  base_url <- "https://api.platform.opentargets.org/api/v4/graphql"
  variables <- list("ensemblId" = gene_id)
  post_body <- list(query = query_string, variables = variables)
  r <- httr::POST(url=base_url, body=post_body, encode='json')
  data <- iconv(r, "", "ASCII")
  content <- jsonlite::fromJSON(data)
  target <- content$data$target
  scalar_fields <- data.frame(
    Field = c("ID", "Approved Symbol", "Biotype"),
    Value = c(target$id, target$approvedSymbol, target$biotype)
  )
  tractability_data <- target$tractability
  kableExtra::kbl(scalar_fields, caption = "(a) Basic Information") %>%
    kableExtra::kable_styling(bootstrap_options = c("striped", "hover"))
  kableExtra::kbl(target$geneticConstraint, caption = "(b) Genetic Constraint Metrics") %>%
    kableExtra::kable_styling(bootstrap_options = c("striped", "hover"))
  kableExtra::kbl(tractability_data, caption = "(c) Tractability Information") %>%
    kableExtra::kable_styling(bootstrap_options = c("striped", "hover"), full_width = FALSE)
}