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rba_reactome_interactors_static.Rd
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rba_reactome_interactors_static.Rd
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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/reactome_content.R
\name{rba_reactome_interactors_static}
\alias{rba_reactome_interactors_static}
\title{Get Static(IntAct) Interaction Information of a Protein}
\usage{
rba_reactome_interactors_static(
proteins,
endpoint = "details",
only_diagrammed = FALSE,
species = NULL,
...
)
}
\arguments{
\item{proteins}{Uniprot proteins accession(s). If endpoint = "pathway",
only a single protein accession can be supplied.}
\item{endpoint}{Can be one of: \enumerate{
\item "details": To return a detailed information of your supplied
protein(s) accession.
\item "summary": To return a summary of your supplied protein(s) accession
\item "pathway": To return a list of pathways containing the interacting
molecules (excluding TopLevelPathway class).}}
\item{only_diagrammed}{Logical: (only when "endpoint = "pathway")
If TRUE, pathways without diagram will be excluded. (default = FALSE)}
\item{species}{Only when "endpoint = "pathway", The scientific name
of the species to search for the pathways. 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{
List which it's content varies based on the supplied "endpoint"
argument.
}
\description{
Reactome maintain a locally host a version of IntAct(Static) interactions
database. Using this function, you can retrieve IntAct information of
a protein(s) in two scenarios: \enumerate{
\item If endpoint = "details" or "summary": Retrieve a detailed/summary
information of your supplied protein accession(s) from IntAct database.
\item If endpoint = "pathway", Retrieve a list of Reactome pathways which
include your supplied protein accession. Pathways with the class
"TopLevelPathway" will be excluded.}
}
\section{Corresponding API Resources}{
"POST https://reactome.org/ContentService/interactors/static/
molecules/details"
\cr "POST https://reactome.org/ContentService/interactors/static/
molecules/summary"
\cr "GET https://reactome.org/ContentService/interactors/static/
molecules/pathways"
}
\examples{
\donttest{
rba_reactome_interactors_static(proteins = "Q9BXM7-1",
endpoint = "pathways", species = "Homo sapiens")
}
\donttest{
rba_reactome_interactors_static(proteins = c("Q9BXM7-1", "Q13501"),
endpoint = "details")
}
\donttest{
rba_reactome_interactors_static(proteins = c("Q9BXM7-1", "Q13501"),
endpoint = "summary")
}
}
\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 - Molecule Interactors":
\code{\link{rba_reactome_interactors_psicquic}()}
}
\concept{"Reactome Content Service - Molecule Interactors"}