rba_reactome_pathways_low.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/reactome_content.R
\name{rba_reactome_pathways_low}
\alias{rba_reactome_pathways_low}
\title{Get lower level pathways Containing a 'Physical Entity' or Event}
\usage{
rba_reactome_pathways_low(
  entity_id,
  with_diagram = FALSE,
  all_forms = FALSE,
  species = NULL,
  ...
)
}
\arguments{
\item{entity_id}{The entity that should exist in the pathways.}

\item{with_diagram}{Logical: only include pathways with diagram?}

\item{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 \code{\link{rba_reactome_participants}}'s
"Details section" to learn more about how Reactome classifies molecules.}

\item{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 \code{\link{rba_reactome_species}} or
 \href{https://reactome.org/content/schema/objects/Species/}{Reactome
 Data Schema: Entries: Species}.}

\item{...}{rbioapi option(s). See \code{\link{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.
}
\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.
}
\section{Corresponding API Resources}{

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

\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)
}

}
\references{
\itemize{
  \item 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
  \item 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.
  \item \href{https://reactome.org/ContentService/}{Reactome Content
  Services API Documentation}
  \item \href{https://reactome.org/cite/}{Citations note on Reactome website}
  }
}
\seealso{
Other "Reactome Content Service - Pathway Related Queries": 
\code{\link{rba_reactome_pathways_events}()},
\code{\link{rba_reactome_pathways_top}()}
}
\concept{"Reactome Content Service - Pathway Related Queries"}