R/AllClasses.R

In chagasVinicius/RTNmotifs: analysis of co-regulatory network motifs and inference of 'dual regulons'.

##------------------------------------------------------------------------------
setClassUnion("TNInull", members = c("TNI", "NULL"))

#' MBR objects
#' 
#' @description 
#' MBR: an S4 class for co-regulation analysis and inference of 'dual 
#' regulons'. 
#'
#' @details 
#' The MBR class is a container for results from the MBR methods. 
#' The class slots are used to store information of different transcriptional networks, 
#' regulator annotation, infered 'dual regulons' and parameters used in the analysis. 
#' All the information is stored in nine slots.
#' 
#' @slot TNI1 a 'TNI' object created by the RTN package.
#' @slot TNI2 another 'TNI' object created by the RTN package.
#' @slot testedElementsTNI1 regulatory elements listed in the TNI1.
#' @slot testedElementsTNI2 regulatory elements listed in the TNI2.
#' @slot dualRegulons all possible 'duals regulons' computed by 
#' \code{\link[RTNduals:mbrAssociation]{mbrAssociation}}
#' @slot results a list, results from the MBR methods.
#' @slot para a list, parameters used in the MBR methods.
#' @slot summary a list, summary for 'para' and 'results'.
#' @slot status a character vector specifying the status of the MBR object 
#' based on the available methods.
#' 
#' @section Constructor:
#' 
#' There are two constructors to create an MBR object, users can opt for one of the following: 
#' (1) \code{\link[RTNduals:mbrPreprocess]{mbrPreprocess}}; 
#' (2) \code{\link[RTNduals:tni2mbrPreprocess]{tni2mbrPreprocess}}.
#' \itemize{
#' \item {(1)}: {It is used to create an MBR object without any pre-computed transcriptional network.}
#' \item {(2)}: {It is used to create an MBR object using available transcriptional networks.} 
#' }
#' 
#' @aliases MBR
#' @exportClass MBR

##Class MBR (Motifs Between Regulons)
setClass(
  "MBR",
  slots=c(
    TNI1="TNInull",
    TNI2="TNInull",
    testedElementsTNI1="character",
    testedElementsTNI2="character",
    dualRegulons="character",
    results="list",
    para='list',
    summary='list',
    status="character"
  ), prototype=list(
    TNI1=NULL,
    TNI2=NULL,
    testedElementsTNI1=character(),
    testedElementsTNI2=character(),
    dualRegulons=character(),
    results=list(),
    para=list(),
    summary=list(),
    status=character()
  )
)