rba_reactome_interactors_static: Get Static(IntAct) Interaction Information of a Protein

Description

Reactome maintain a locally host a version of IntAct(Static) interactions database. Using this function, you can retrieve IntAct information of a protein(s) in two scenarios:

If endpoint = "details" or "summary": Retrieve a detailed/summary information of your supplied protein accession(s) from IntAct database.
If endpoint = "pathway", Retrieve a list of Reactome pathways which include your supplied protein accession. Pathways with the class "TopLevelPathway" will be excluded.

Usage

rba_reactome_interactors_static(
  proteins,
  endpoint = "details",
  only_diagrammed = FALSE,
  species = NULL,
  ...
)

Value

List which it's content varies based on the supplied "endpoint" argument.

Arguments

proteins

Uniprot proteins accession(s). If endpoint = "pathway", only a single protein accession can be supplied.

endpoint

Can be one of:

"details": To return a detailed information of your supplied protein(s) accession.
"summary": To return a summary of your supplied protein(s) accession
"pathway": To return a list of pathways containing the interacting molecules (excluding TopLevelPathway class).

only_diagrammed

Logical: (only when "endpoint = "pathway") If TRUE, pathways without diagram will be excluded. (default = FALSE)

species

Only when "endpoint = "pathway", The scientific name of the species to search for the pathways. See rba_reactome_species or Reactome Data Schema: Entries: Species.

...

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

Corresponding API Resources

"POST https://reactome.org/ContentService/interactors/static/ molecules/details"
"POST https://reactome.org/ContentService/interactors/static/ molecules/summary"
"GET https://reactome.org/ContentService/interactors/static/ molecules/pathways"

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 Content Services API Documentation
Citations note on Reactome website

Examples

Run this code

# \donttest{
rba_reactome_interactors_static(proteins = "Q9BXM7-1",
    endpoint = "pathways", species = "Homo sapiens")
# }
# \donttest{
rba_reactome_interactors_static(proteins = c("Q9BXM7-1", "Q13501"),
    endpoint = "details")
# }
# \donttest{
rba_reactome_interactors_static(proteins = c("Q9BXM7-1", "Q13501"),
    endpoint = "summary")
# }

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