R/simulateSteadyState.R

In mccallm/ternarynet: Ternary Network Estimation

getObservedAttractor <- function(perturbations, tableObj, graphObj, degreeObj, wildtype) {
  fg <- perturbations$perturbed.genes
  fs <- perturbations$forced.states + 2
  tn.model <- list(table = tableObj + 2, graph = graphObj, degree = degreeObj)
  vec0 <- rep(2, length(tn.model$degree))
  vec0[fg] <- fs
  junk <- attractor.distance.summary(vec0, tn.model, wildtype, fg, fs)
  nc <- dim(junk$attractor)[2]
  return(summarize.attractor.2(junk$attractor[, 2:nc]))
}

simulateSteadyState <- function(perturbationObj, tableObj, graphObj, degreeObj, wildtype = FALSE) {
  steadyStateObj <- matrix(nrow = nrow(perturbationObj), ncol = ncol(perturbationObj))
  for (k in seq_len(ncol(perturbationObj))) {
    ind <- which(perturbationObj[, k] != 0)
    perts <- list("perturbed.genes" = ind, "forced.states" = perturbationObj[ind, k])
    steadyStateObj[, k] <- getObservedAttractor(perts, tableObj, graphObj, degreeObj, wildtype)
  }
  return(steadyStateObj)
}