rbioapi: rba_reactome_interactors_static – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

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 provided protein accession(s) from IntAct database.
If endpoint = "pathway", Retrieve a list of Reactome pathways which include your provided protein accession. Pathways with the class "TopLevelPathway" will be excluded.

Usage

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

Arguments

`proteins`	Uniprot proteins accession(s). If endpoint = "pathway", only a single protein accession can be provided.
`endpoint`	Can be one of: "details": To return a detailed information of your provided protein(s) accession. "summary": To return a summary of your provided 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. Refer to `rba_reactome_species` or Reactome Data Schema: Entries: Species.
`...`	rbioapi option(s). Refer to `rba_options`'s arguments documentation for more information on available options.

Value

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

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

Jassal B, Matthews L, Viteri G, Gong C, Lorente P, Fabregat A, Sidiropoulos K, Cook J, Gillespie M, Haw R, Loney F, May B, Milacic M, Rothfels K, Sevilla C, Shamovsky V, Shorser S, Varusai T, Weiser J, Wu G, Stein L, Hermjakob H, D'Eustachio P. The reactome pathway knowledgebase. Nucleic Acids Res. 2020 Jan 8;48(D1):D498-D503. doi: 10.1093/nar/gkz1031. PubMed PMID: 31691815.
Reactome Content Services API Documentation

Examples

rba_reactome_interactors_static(proteins = "Q9BXM7-1",
    endpoint = "pathways", species = "Homo sapiens")


rba_reactome_interactors_static(proteins = c("Q9BXM7-1", "Q13501"),
    endpoint = "details")


rba_reactome_interactors_static(proteins = c("Q9BXM7-1", "Q13501"),
    endpoint = "summary")

rbioapi

User-Friendly R Interface to Biologic Web Services' API

v0.7.0

GPL-3

Authors

Moosa Rezwani [aut, cre, cph]

Initial release