rbioapi: rba_reactome_pathways_low – R documentation

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

rba_reactome_pathways_low

Get lower level pathways Containing a 'Physical Entity' or Event

Description

Use this function to search the event hierarchy and retrieve a list of all lower level pathways (non TopLevelPathway class) that contain a given 'Physical Entity' or Event. See "Arguments section" on how to modify your search.

Usage

rba_reactome_pathways_low(
  entity_id,
  with_diagram = FALSE,
  all_forms = FALSE,
  species = NA,
  ...
)

Arguments

`entity_id`	The entity that should exist in the pathways.
`with_diagram`	Logical: only include pathways with diagram?
`all_forms`	Logical: should other variants of your provided entity_id be considered? (e.g. same molecule but in different compartment, secretory form etc.) refer to `rba_reactome_participants`'s "Details section" to learn more about how Reactome classifies molecules.
`species`	(optional) Numeric or Character: confine your search to a specific species by providing it's NCBI Taxonomy identifier (Human Taxonomy ID is 9606) or species name (e.g. "Homo sapiens"). 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 that contains your provided entity and columns are pertinent information.

Corresponding API Resources

"GET https://reactome.org/ContentService/data/pathways/low/entity/id"
"GET https://reactome.org/ContentService/data/pathways/low/diagram/ entity/id"
"GET https://reactome.org/ContentService/data/pathways/low/diagram/ entity/id/allForms"

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_pathways_low(entity_id = "R-HSA-199420")


rba_reactome_pathways_low(entity_id = "R-HSA-199420", with_diagram = TRUE)


rba_reactome_pathways_low(entity_id = "R-HSA-199420", with_diagram = TRUE,
    all_forms = TRUE)

rbioapi

User-Friendly R Interface to Biologic Web Services' API

v0.7.0

GPL-3

Authors

Moosa Rezwani [aut, cre, cph]

Initial release