R/keggInteractome.R

In fernandoPalluzzi/SEMgraph: Network Analysis and Causal Inference Through Structural Equation Modeling

#  SEMgraph library
#  Copyright (C) 2019-2021 Mario Grassi; Fernando Palluzzi; Barbara Tarantino
#  e-mail: <mario.grassi@unipv.it>
#  University of Pavia, Department of Brain and Behavioral Sciences
#  Via Bassi 21, 27100 Pavia, Italy

#  SEMgraph is free software: you can redistribute it and/or modify
#  it under the terms of the GNU General Public License as published by
#  the Free Software Foundation, either version 3 of the License, or
#  (at your option) any later version.

#  SEMgraph is distributed in the hope that it will be useful,
#  but WITHOUT ANY WARRANTY; without even the implied warranty of
#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#  GNU General Public License for more details.

#  You should have received a copy of the GNU General Public License
#  along with this program.  If not, see <https://www.gnu.org/licenses/>.

# -------------------------------------------------------------------- #

#' @title KEGG interactome
#'
#' @description Interactome generated by merging KEGG pathways 
#' extracted using the \code{ROntoTools} R package (update: Jan, 2025).
#' @name kegg
#' @usage kegg
#' @docType data
#' @format
#' "kegg" is an igraph network object of 4910 nodes and 45200 edges 
#' corresponding to the union of 231 KEGG pathways.
#' @source \url{https://www.genome.jp/kegg/}
#' @references
#' 
#' Kanehisa M, Goto S (1999). KEGG: kyoto encyclopedia of genes and genomes. 
#' Nucleic Acid Research 28(1): 27-30. 
#' <https://doi.org/10.1093/nar/27.1.29>
#'
#' Calin Voichita, Sahar Ansari and Sorin Draghici (2023).
#' ROntoTools: R Onto-Tools suite. R package version 2.30.0.
#'
#' @examples
#' 
#' # KEGG graph
#' summary(kegg)
#' 
#' # KEGG degrees of freedom
#' vcount(kegg)*(vcount(kegg) - 1)/2 - ecount(kegg)
#'
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