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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

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

  • Marc Gillespie, Bijay Jassal, Ralf Stephan, Marija Milacic, Karen Rothfels, Andrea Senff-Ribeiro, Johannes Griss, Cristoffer Sevilla, Lisa Matthews, Chuqiao Gong, Chuan Deng, Thawfeek Varusai, Eliot Ragueneau, Yusra Haider, Bruce May, Veronica Shamovsky, Joel Weiser, Timothy Brunson, Nasim Sanati, Liam Beckman, Xiang Shao, Antonio Fabregat, Konstantinos Sidiropoulos, Julieth Murillo, Guilherme Viteri, Justin Cook, Solomon Shorser, Gary Bader, Emek Demir, Chris Sander, Robin Haw, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D’Eustachio, The reactome pathway knowledgebase 2022, Nucleic Acids Research, 2021;, kab1028, https://doi.org/10.1093/nar/gkab1028

  • Griss J, Viteri G, Sidiropoulos K, Nguyen V, Fabregat A, Hermjakob H. ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis. Mol Cell Proteomics. 2020 Sep 9. doi: 10.1074/mcp. PubMed PMID: 32907876.

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