R/buildDataMatrix.R

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

#'\code{buildDataMatrix}
#'
#'This function returns the data matrix containing the data for running CARNIVAL 
#'and a set of identifiers for Targets, Measured and Un-measured nodes.
#'
#'Enio Gjerga, 2020

buildDataMatrix <- function(data = data, pknList = pknList, inputs = inputs) {

  colnames(pknList) <- c("X1", "X2", "X3")
  allSpecies <- unique(c(as.character(pknList$X1), as.character(pknList$X3)))

  if(ncol(inputs) > 0){

    ts <- intersect(colnames(inputs), allSpecies)

  }

  ds <- intersect(colnames(data), allSpecies)

  dn <- setdiff(allSpecies, ds)

  dataMatrix <- matrix(0, nrow = nrow(data), ncol = length(allSpecies))

  dnNames <- paste0("DN:", dn)
  dsNames <- paste0("DS:", ds)

  colnames(dataMatrix) <- c(dnNames, dsNames)

  if(length(which(is.element(el = colnames(data), 
                             set = setdiff(colnames(data), ds)))) > 0){

    dataMatrix[, (length(dn)+1):length(allSpecies)] <- 
      as.matrix(data[, -which(is.element(el = colnames(data), 
                                         set = setdiff(colnames(data), ds)))])

  }
  else{

    dataMatrix[, (length(dn)+1):length(allSpecies)] <- as.matrix(data)

  }

  dataMatrixSign <- sign(dataMatrix)

  dnID <- 1:length(dn)
  dsID <- (length(dn)+1):length(allSpecies)
  tsID <- which(is.element(el = c(dn, ds), set = ts))

  res <- list(dataMatrix=dataMatrix, dataMatrixSign=dataMatrixSign, dnID=dnID, 
              dsID=dsID, tsID=tsID, species=c(dn, ds))

  return(res)

}