R/transformBinaries.R

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

## Vectorizing the binaries
##
## Enio Gjerga, 2020

transformBinaries <- function(mt = mt, lpFile = lpFile){
  
  idx1 <- which(lpFile$`enter Problem`=="Binaries")
  idx2 <- which(lpFile$`enter Problem`=="Generals")
  
  constraintSet <- lpFile$`enter Problem`[seq(from = idx1+1, 
                                              to = idx2-1, by = 1)]
  
  f.con <- matrix(data = 0, nrow = 2*length(constraintSet), ncol = nrow(mt))
  ## f.dir <- c()
  ## f.rhs <- c()
  f.dir <- rep("", length(constraintSet)*2)
  f.rhs <- rep("", length(constraintSet)*2)
  
  cnt <- 1
  for(ii in seq_len(length(constraintSet))){
    
    currConstraint <- constraintSet[ii]
    
    f.con[cnt, which(mt[, 1]==currConstraint)] <- 1
    f.dir[cnt] <- ">="
    f.rhs[cnt] <- 0
    cnt <- cnt + 1
    f.con[cnt, which(mt[, 1]==currConstraint)] <- 1
    f.dir[cnt] <- "<="
    f.rhs[cnt] <- 1
    cnt <- cnt + 1
    
  }
  
  ff <- vector(mode = "list", length = 3)
  names(ff) <- c("con", "dir", "rhs")
  ff$con <- f.con
  ff$dir <- f.dir
  ff$rhs <- f.rhs
  
  return(ff)
  
}