R/tnetfit.R

In mccallm/ternarynet: Ternary Network Estimation

tnetfit <- function(steadyStateObj, perturbationObj, params = ternaryFitParameters(), xSeed = NA) {
  if (!identical(rownames(steadyStateObj), rownames(perturbationObj))) stop("steadyStateObj and perturbationObj must have identical rownames")
  if (!identical(colnames(steadyStateObj), colnames(perturbationObj))) stop("steadyStateObj and perturbationObj must have identical colnames")

  if (is.null(rownames(steadyStateObj))) gNames <- paste("Gene", seq_len(nrow(steadyStateObj)), sep = "") else gNames <- rownames(steadyStateObj)
  if (is.null(colnames(steadyStateObj))) expNames <- paste("Exp", seq_len(ncol(steadyStateObj)), sep = "") else expNames <- colnames(steadyStateObj)

  nGene <- as.integer(nrow(steadyStateObj))
  nExperiment <- as.integer(ncol(steadyStateObj))

  ssObj <- as.vector(t(steadyStateObj)) + 2
  pObj <- as.integer(t(perturbationObj) + 2)

  if (is.na(xSeed)) xSeed <- as.integer(floor(runif(1) * 10000))
  ### set.seed(xSeed) # removed to make BiocCheck happy - HAS 4/12/2021

  tmp <- .Call("tnetfit", as.integer(perturbationType(params)), as.integer(scoreType(params)), as.integer(backupStage(params)), as.integer(maxStage(params)), as.integer(maxTransition(params)), epsilon(params), as.integer(beta0(params)), chi0(params), delta(params), as.integer(ne(params)), as.integer(m0(params)), as.integer(maxDegree(params)), pAddParent(params), pExchangeParent(params), as.integer(neighborDegree(params)), pNeighborhood(params), rho(params), nGene, nExperiment, edgePenalty(params), ssObj, pObj)

  traces <- data.frame(muTrace = tmp$muTrace, sigmaTrace = tmp$sigmaTrace, sigmaRhoTrace = tmp$sigmaRhoTrace, temperatureTrace = tmp$temperatureTrace)

  ternaryFit(perturbationObj = perturbationObj, steadyStateObj = steadyStateObj, geneNames = gNames, experimentNames = expNames, degreeObjMin = tmp$degreeObjMin, graphObjMin = matrix(tmp$graphObjMin, nrow = nGene), tableObjMin = matrix(tmp$tableObjMin, ncol = nGene), newScore = tmp$newScore, minScore = tmp$minScore, finalTemperature = tmp$scTemperature, traces = traces, stageCount = tmp$stageCount, xSeed = as.integer(xSeed), inputParams = params)
}