Skip to contents

Return the Results Associated with a Token

Source: R/reactome_analysis.R
rba_reactome_analysis_token.Rd

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 = NULL,
  sort_by = "ENTITIES_PVALUE",
  order = "ASC",
  resource = "TOTAL",
  p_value = 1,
  include_disease = TRUE,
  min = NULL,
  max = NULL,
  ...
)

Arguments

token

Character: A token associated to your previous Reactome analysis.

species

Character or Numeric: (optional) 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

Character: (default = "ENTITIES_PVALUE") 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

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

resource

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

p_value

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

include_disease

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

min

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

max

Numeric: (optional) 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

A list containing the results and information about the analysis. The pathways element is a data frame with information about each pathway expanded into columns; it is an empty data frame when no pathways match. Its structure is the same as the output from rba_reactome_analysis.

Details

After any analysis, Reactome will associate a token with your analysis. It can later be used in functions that require 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

  • 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

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

Examples

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