Get lower level pathways Containing a 'Physical Entity' or EventSource:
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.
rba_reactome_pathways_low( entity_id, with_diagram = FALSE, all_forms = FALSE, species = NULL, ... )
The entity that should exist in the pathways.
Logical: only include pathways with diagram?
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.
(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_speciesor Reactome Data Schema: Entries: Species.
rbioapi option(s). See
rba_options's arguments manual for more information on available options.
Data frame where each row is a pathway that contains your supplied entity and columns are pertinent information.
"GET https://reactome.org/ContentService/data/pathways/low/diagram/ entity/id"
"GET https://reactome.org/ContentService/data/pathways/low/diagram/ entity/id/allForms"
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.