R/write_constraints_8.R

In saezlab/CARNIVAL-Bioconductor-Dev: A CAusal Reasoning tool for Network Identification (from gene expression data) using Integer VALue programming

#'\code{write_constraints_8}
#'
#' This code writes the list of constraints (8) of the ILP problem for all the 
#' conditions.
#' 
#' Enio Gjerga, 2020

write_constraints_8 <- function(variables=variables, 
                                inputs=inputs, 
                                pknList=pknList){
  
  constraints8 <- c()
  
  for(ii in 1:length(variables)){
    
    ##
    cc <- paste0(
      variables[[ii]]$variables[variables[[ii]]$idxNodesUp], 
      " - ", 
      variables[[ii]]$variables[variables[[ii]]$idxNodesDown], 
                 " + ", variables[[ii]]$variables[variables[[ii]]$idxB], 
      " - ", variables[[ii]]$variables[variables[[ii]]$idxNodes], " = 0")
    
    constraints8 <- c(constraints8, cc)
    
    ##
    kk <- paste0("Species ", colnames(inputs), " in experiment ", ii)
    cc <- paste0(
      variables[[ii]]$variables[variables[[ii]]$idxB[which(
        !(variables[[ii]]$exp[variables[[ii]]$idxNodes] %in% kk))]], " = 0")
    constraints8 <- c(constraints8, cc)
    
    ##
    kk <- paste0("Species ", colnames(inputs), " in experiment ", ii)
    cc= c()
    for(jj in 1:length(kk)){
      cName = strsplit(x = kk[jj], split = " ")[[1]][2]
      cc = c(cc, paste0(
        variables[[ii]]$variables[which(
          variables[[ii]]$exp==paste0(
            "Species ", cName, " in experiment ", ii))], " = ", inputs[ii, jj]))
    }
    constraints8 <- c(constraints8, cc)
    
    ##
    if (length(
      setdiff(
        as.character(pknList[, 1]), 
        as.character(pknList[, 3])))>0) {
      kk <- paste0(
        "Species ", 
        setdiff(as.character(pknList[, 1]), 
                as.character(pknList[, 3])), " in experiment ", ii)
      cc <- paste0(
        variables[[ii]]$variables[variables[[ii]]$idxNodes[which(
          variables[[ii]]$exp[variables[[ii]]$idxNodes] %in% kk)]], " - ", 
                   variables[[ii]]$variables[variables[[ii]]$idxB[which(
                     variables[[ii]]$exp[variables[[ii]]$idxNodes] %in% kk)]], 
        " = 0")
      constraints8 <- c(constraints8, cc)
    }
    
  }
  
  return(constraints8)
  
}