rbioapi: rba_reactome_mapping – R documentation

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rba_reactome_mapping

Map External ID to Reactome Pathways/Reactions

Description

By providing an external identifier from a given resource, you can retrieve a list of pathways/reactions that include your provided ID.

Usage

rba_reactome_mapping(id, resource, map_to, species = "Homo sapiens", ...)

Arguments

`id`	Molecule's external Identifier
`resource`	What is the resource of your provided ID? see: Reactome External Identifiers
`map_to`	Either "pathways" or "reactions".
`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.
`...`	rbioapi option(s). Refer to `rba_options`'s arguments documentation for more information on available options.

Value

Data frame where each row is a pathway/reaction and columns are pertinent information.

Corresponding API Resources

"GET https://reactome.org/ContentService/data/mapping/resource/ identifier/pathways"
"GET https://reactome.org/ContentService/data/mapping/resource/ identifier/reactions"

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_mapping(id = "PTEN", resource =  "UniProt",
    map_to = "reactions", species = 9606)

rbioapi

User-Friendly R Interface to Biologic Web Services' API

v0.7.0

GPL-3

Authors

Moosa Rezwani [aut, cre, cph]

Initial release