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

Source: R/reactome_content.R
rba_reactome_pathways_low.Rd

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 = NULL,
  ...
)

Arguments

entity_id

Character: The entity that should exist in the pathways.

with_diagram

Logical: (default = FALSE) only include pathways with diagram?

all_forms

Logical: (default = FALSE) should other variants of your supplied entity_id be considered? (e.g. same molecule but in different compartment, secretory form etc.) see rba_reactome_participants's "Details section" to learn more about how Reactome classifies molecules.

species

Character or Numeric: (optional) 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"). 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.

Value

Data frame where each row is a pathway that contains your supplied 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

  • Ragueneau, E., Gong, C., Sinquin, P., Sevilla, C., Beavers, D., Grentner, A., ... D’Eustachio, P. (2026). The Reactome Knowledgebase 2026. Nucleic Acids Res., 54(D1), D673–D681. doi: 10.1093/nar/gkaf1223

  • Griss, J., Viteri, G., Sidiropoulos, K., Nguyen, V., Fabregat, A., & Hermjakob, H. (2020). ReactomeGSA—Efficient Multi-Omics Comparative Pathway Analysis. Molecular & Cellular Proteomics, 19(12), 2115–2125. doi: 10.1074/mcp.TIR120.002155

  • Reactome Content Services API Documentation

  • Citations note on Reactome website

See also

Other "Reactome Content Service - Pathway Related Queries": rba_reactome_pathways_events(), rba_reactome_pathways_top()

Examples

# \donttest{
rba_reactome_pathways_low(entity_id = "R-HSA-199420")
# }
# \donttest{
rba_reactome_pathways_low(entity_id = "R-HSA-199420", with_diagram = TRUE)
# }
# \donttest{
rba_reactome_pathways_low(entity_id = "R-HSA-199420", with_diagram = TRUE,
    all_forms = TRUE)
# }