R/AllClass.R

In YuanlongHu/immcp: Poly-Pharmacology Toolkit for Traditional Chinese Medicine Research

# register the S3 `igraph` class for use with S4 methods.
#' @import methods
setOldClass("igraph", igraph::make_empty_graph())
selectMethod("show", "igraph")

#' Class \code{BasicData}
#' This class represents the basic input data.
#'
#'
#' @name BasicData-class
#' @docType class
#' @slot drugnet A directed graph
#' @slot diseasenet Disease network.
#' @slot biomarker Disease-related gene.
#' @exportClass BasicData
#' @author Yuanlong Hu

setClass("BasicData",
         slots = list(
           drugnet = "igraph",
           #vertices = "data.frame",
           diseasenet = "igraph",
           biomarker = "list"
         ))

#' Class \code{BioDescr}
#' This class represents the biological descriptor data.
#'
#'
#' @name BioDescr-class
#' @docType class
#' @slot drug_geneset from drug to geneset.
#' @slot geneset_gene from geneset to gene for each drug.
#' @slot anno Geneset ID and description.
#' @exportClass BioDescr
#' @author Yuanlong Hu

setClass("BioDescr",
         slots = list(
           drug_geneset = "igraph",
           geneset_gene = "list",
           anno = "data.frame"
         ))


#' Class \code{HerbResult}
#' This class represents the biological descriptor data.
#'
#'
#' @name HerbResult-class
#' @docType class
#' @slot Drug_Herb Data frame, Drug-herb relationship.
#' @slot Herb_Herb Herb-herb association Rule Graph, it is a directed graph.
#' @exportClass HerbResult
#' @author Yuanlong Hu

setClass("HerbResult",
         slots = list(
           Drug_Herb = "data.frame",
           Herb_Herb = "igraph"
         ))