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Download Different Reactome Analysis Results

Source: R/reactome_analysis.R
rba_reactome_analysis_download.Rd

Based on the "request" argument, you can download different analysis results data associated with a given token.

Usage

rba_reactome_analysis_download(
  token,
  request,
  save_to = NULL,
  resource = "TOTAL",
  ...
)

Arguments

token

Character: A token associated to your previous Reactome analysis.

request

Character: What to download? Should be one of:

  • "found_ids": Download a CSV file containing the found user-supplied identifiers in the analysis associated with your supplied token and resource.

  • "not_found_ids"" Download a CSV file containing the user-supplied Identifiers which has not been found in the analysis associated with your supplied token.

  • "pathways": Download a CSV file containing Pathway analysis results of the analysis associated with your supplied token and resource.

  • "results": Download a JSON file containing the complete analysis results associated with your supplied token.

  • "results_gz" Same as "results", but the output will be compress (gzipped).

save_to

NULL or Character: (optional)

  • NULL: Save the file to an automatically-generated path.

  • Character string: A valid file path to save the file to.

resource

Character: (default = "TOTAL") (Only when request is "found_ids" or "pathways") Filter results based on the resource. Available choices are:"TOTAL", "UNIPROT", "ENSEMBL", "CHEBI", "IUPHAR", "MIRBASE", "NCBI_PROTEIN", "EMBL", "COMPOUND" or "PUBCHEM_COMPOUND".

...

rbioapi option(s). See rba_options's arguments manual for more information on available options.

Value

NULL, a CSV,JSON or Gzipped JSON file will be saved to disk based on your input.

Details

Token is associated to each Reactome analysis results and kept by Reactome for at least 7 days. You can locate it in rba_reactome_analysis's output, under a sub-list named "summary" (i.e. results$summary$token).
Use rba_reactome_analysis_pdf to save a full report in PDF format.

Corresponding API Resources

GET https://reactome.org/AnalysisService/download/{token}/entities/ found/{resource}/{filename}.csv"
GET https://reactome.org/AnalysisService/download/{token}/entities/ notfound/{filename}.csv"
GET https://reactome.org/AnalysisService/download/{token}/pathways/ {resource}/{filename}.csv"
GET https://reactome.org/AnalysisService/download/{token}/result.json"
GET https://reactome.org/AnalysisService/download/{token}/result.json.gz"

References

  • Ragueneau, E., Gong, C., Sinquin, P., Sevilla, C., Beavers, D., Grentner, A., ... D’Eustachio, P. (2026). The Reactome Knowledgebase 2026. Nucleic Acids Res., 54(D1), D673–D681. doi: 10.1093/nar/gkaf1223

  • Griss, J., Viteri, G., Sidiropoulos, K., Nguyen, V., Fabregat, A., & Hermjakob, H. (2020). ReactomeGSA—Efficient Multi-Omics Comparative Pathway Analysis. Molecular & Cellular Proteomics, 19(12), 2115–2125. doi: 10.1074/mcp.TIR120.002155

  • Reactome Analysis Services API Documentation

  • Citations note on Reactome website

See also

rba_reactome_analysis_pdf rba_reactome_analysis

Other "Reactome Analysis Service": rba_reactome_analysis(), rba_reactome_analysis_import(), rba_reactome_analysis_mapping(), rba_reactome_analysis_pdf(), rba_reactome_analysis_species(), rba_reactome_analysis_token()

Examples

if (FALSE) { # \dontrun{
rba_reactome_analysis_download(token = "MjAyMDEwMTYwMTI3MTNfMjY1MjM",
    request = "pathways", save_to = "found_ids.csv")
} # }
if (FALSE) { # \dontrun{
rba_reactome_analysis_download(token = "MjAyMDEwMTYwMTI3MTNfMjY1MjM",
    request = "found_ids", save_to = "found_ids.csv")
} # }