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Use a token generated After a Reactome analysis (via rba_reactome_analysis) to Retrieve the analysis results. The output format is identical to the returned object of rba_reactome_analysis.

Usage

rba_reactome_analysis_token(
  token,
  species,
  sort_by = "ENTITIES_PVALUE",
  order = "ASC",
  resource = "TOTAL",
  p_value = NULL,
  include_disease = TRUE,
  min = NULL,
  max = NULL,
  ...
)

Arguments

token

A token associated to your previous Reactome analysis.

species

Numeric or Character: NCBI Taxonomy identifier (Human is 9606), species name (e.g. "Homo sapiens") or Reactome DbId (e.g Homo sapiens is 48887). See rba_reactome_species or Reactome Data Schema: Entries: Species.

sort_by

Sort the result based on what column? available choices are: "NAME", "TOTAL_ENTITIES", "TOTAL_INTERACTORS", "TOTAL_REACTIONS", "FOUND_ENTITIES", "FOUND_INTERACTORS", "FOUND_REACTIONS", "ENTITIES_RATIO", "ENTITIES_PVALUE", "ENTITIES_FDR" or "REACTIONS_RATIO"

order

Sort Order. Can be either "ASC" (default) or "DESC".

resource

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".

p_value

Set a P value threshold. Only results with P value equal to or less than your supplied threshold will be returned. (default = 1, Meaning no P value filtering)

include_disease

Logical (default = TRUE) Should the disease pathways be included in the results?

min

(numeric) Minimum number of entities that a pathways should have to be included in the results.

max

(numeric) Maximum number of entities that a pathways should have to be included in the results.

...

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

Value

List containing the results and information of your analysis.

Details

After Any Analysis, Reactome will associate a token to your analysis. It can be later used to in function that requires the token (e.g to retrieve the analysis results, download pdf).
Note that Reactome will store your token for only 7 days. You can download your full results with rba_reactome_analysis_download, and re-import it anytime to reactome (using rba_reactome_analysis_import) to generate a new token.

Corresponding API Resources

"GET https://reactome.org/AnalysisService/token/token"

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

Examples

if (FALSE) {
rba_reactome_analysis_token(token = "MjAyMDEwMTYwMTI3MTNfMjY1MjM",
    species = 9606)
}