rbioapi: rba_reactome_analysis_token – R documentation

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rba_reactome_analysis_token

Return the Results Associated with a Token

Description

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 = NA,
  include_disease = TRUE,
  min = NA,
  max = NA,
  ...
)

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). Refer to `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 provided 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). Refer to `rba_options`'s arguments documentation for more information on available options.

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.

Value

List containing the results and information of your analysis.

Corresponding API Resources

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

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

Examples

## Not run: 
rba_reactome_analysis_token(token = "MjAyMDEwMTYwMTI3MTNfMjY1MjM",
    species = 9606)

## End(Not run)

rbioapi

User-Friendly R Interface to Biologic Web Services' API

v0.7.0

GPL-3

Authors

Moosa Rezwani [aut, cre, cph]

Initial release