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

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

Arguments

token

A token associated to your previous Reactome analysis.

request

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:

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

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

resource

(Only when request is "found_ids" or "pathways") Filter results based on the resource. Default is "TOTAL", available choices are:"TOTAL", "UNIPROT", "ENSEMBL", "CHEBI", "IUPHAR", "MIRBASE", "NCBI_PROTEIN", "EMBL", "COMPOUND", "ENTITIES_FDR" 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

  • Fabregat A, Sidiropoulos K, Viteri G, Forner O, Marin-Garcia P, Arnau V, D'Eustachio P, Stein L, Hermjakob H. Reactome pathway analysis: a high-performance in-memory approach. BMC bioinformatics. 2017 Mar;18(1) 142. doi: 10.1186/s12859-017-1559-2. PubMed PMID: 28249561. PubMed Central PMCID: PMC5333408.

  • Reactome Analysis Services API Documentation

See also

Examples

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