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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

The entity that should exist in the pathways.

with_diagram

Logical: only include pathways with diagram?

all_forms

Logical: 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

(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"). 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

  • 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

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)
# }