R/write_constraints_4.R

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

## This code writes the list of constraints (4) of the ILP problem for one 
## condition.
## 
## Enio Gjerga, 2020

write_constraints_4 <- function(variables=variables, 
                                conditionIDX=conditionIDX) {
  
  constraints4 <- rep("", length(variables$idxEdgesUp))
  
  idx1 <- which(variables$signs==1)
  idx2 <- which(variables$signs==-1)
  
  constraints4[idx1] <- paste0(
    variables$variables[variables$idxEdgesUp[idx1]], 
    " - ",
    variables$variables[match(
      paste0(
        "Species ",
        unlist(
          strsplit(
            gsub(
              gsub(
                variables$exp[variables$idxEdgesUp[idx1]], 
                pattern = "ReactionUp ", 
                replacement = ""), 
              pattern = paste0(
                " in experiment ", 
                conditionIDX), 
              replacement = ""), 
            split = "="))[c(TRUE, FALSE)],
        " in experiment ", 
        conditionIDX), 
      variables$exp)], 
    " - ",
    variables$uTable[match(
      variables$variables[variables$idxEdgesUp[idx1]], 
      variables$uTable[, 1]), 2], " <= 0")
  
  constraints4[idx2] <- paste0(
    variables$variables[variables$idxEdgesUp[idx2]], 
    " + ",
    variables$variables[match(
      paste0(
        "Species ",
        unlist(
          strsplit(
            gsub(
              gsub(
                variables$exp[variables$idxEdgesUp[idx2]], 
                pattern = "ReactionUp ", 
                replacement = ""), 
              pattern = paste0(
                " in experiment ", 
                conditionIDX), 
              replacement = ""), 
            split = "="))[c(TRUE, FALSE)],
        " in experiment ", 
        conditionIDX), 
      variables$exp)], 
    " - ",
    variables$uTable[match(
      variables$variables[variables$idxEdgesUp[idx2]], 
      variables$uTable[, 1]), 2], " <= 0")
  
  return(constraints4)
  
}