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A Reactome Event could be comprised of other events (meaning, a pathway that include other pathways itself). Use this function to recursively return all the events which reside downstream of your supplied event ID (or an attribute of that events).

Usage

rba_reactome_pathways_events(event_id, attribute_name = NULL, ...)

Arguments

event_id

Reactome event's database ID (DbId) or Stable ID (StId).

attribute_name

An attribute of the events to be returned instead of the whole events. see Reactome Data Schema: Event for available options.

...

rbioapi option(s). See rba_options's arguments manual for more information on available options.

Value

Data frame where each row is a contained event and columns are event's attributes. If an "attribute_name" argument was supplied, a character vector will be returned.

Details

By Reactome's definition, Events are the building blocks of biological processes and could be of two main classes: "Pathway" or "Reaction-like events". The events are organized in a hierarchical structure; and each event could be child or parent to another event; The hierarchy will always begin with a "Top level pathway" event. Also note that a given event could be part of more that one hierarchies.

Corresponding API Resources

"GET https://reactome.org/ContentService/data/pathway/id/ containedEvents"
"GET https://reactome.org/ContentService/data/pathway/id/ containedEvents/attributeName"

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_low(), rba_reactome_pathways_top()

Examples

# \donttest{
rba_reactome_pathways_events(event_id = "R-HSA-5673001")
# }
# \donttest{
rba_reactome_pathways_events(event_id = "R-HSA-5673001",
    attribute_name = "displayName")
# }