Get Open Targets — get_opentargets • KGExplorer

Get Open Targets disease-gene associations data NOTE: If you get an error like " Cannot call parquet...", try running arrow::install_arrow, restarting the R session, and trying again.

get_opentargets(
  release = "latest",
  data_type = c("associationByDatasourceDirect", "associationByDatasourceIndirect",
    "associationByDatatypeDirect", "associationByDatatypeIndirect",
    "associationByOverallDirect", "associationByOverallIndirect", "l2g")[1],
  server = "https://ftp.ebi.ac.uk/pub/databases/opentargets/",
  subdir = c("platform/", "genetics/")[1],
  subdir2 = c("/output/etl/parquet/", "/")[1],
  ftp = paste0(server, subdir, release, subdir2, data_type[1], "/"),
  save_dir = cache_dir(),
  force_new = FALSE
)

Source

OpenTargets GraphQL queries in R

Arguments

release: Open Targets release version.
data_type: Type of data to download.
server: Open Targets server.
subdir: Open Targets subdirectory.
subdir2: Open Targets sub-subdirectory.
ftp: The final Open Targets FTP URL.
save_dir: Directory to save a file to.
force_new: If TRUE, force a new download.

Examples

d <- get_opentargets()
#> 3 core(s) assigned as workers (1 reserved).
#> 
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#> 
#> OpenTargets data loaded with: 
#> - 2,882,629 rows 
#> - 30,315 unique targets across 
#> - 17,701 unique diseases across
#> Caching file --> /github/home/.cache/R/KGExplorer/opentargets_associationByDatasourceDirect.rds