Return the Results Associated with a TokenSource:
rba_reactome_analysis_token( token, species, sort_by = "ENTITIES_PVALUE", order = "ASC", resource = "TOTAL", p_value = NULL, include_disease = TRUE, min = NULL, max = NULL, ... )
A token associated to your previous Reactome analysis.
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_speciesor Reactome Data Schema: Entries: Species.
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"
Sort Order. Can be either "ASC" (default) or "DESC".
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".
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)
Logical (default = TRUE) Should the disease pathways be included in the results?
(numeric) Minimum number of entities that a pathways should have to be included in the results.
(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.
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
rba_reactome_analysis_import) to generate
a new token.
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.