R/assignPROGENyScores.R

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

#'\code{assignPROGENyScores}
#'
#'@param progeny contains the progeny scores as obtained from \code{runPROGENy}.
#'@param progenyMembers contains the list of members for each PROGENy pathway.
#'@param id contains the members identifiers (default: gene).
#'@param access_idx index of the sample to consider (default set to 
#'access_idx = 1)
#'
#'@return This function is used to account for the PROGENy scores in the 
#'objective function. It creates a list object with progeny scores for a 
#'selected set of samples (by default for all of them)
#'
#'@export
#'
#'Enio Gjerga & Panuwat Trairatphisan, 2020

assignPROGENyScores <- function(progeny = progeny, 
                                progenyMembers = progenyMembers, 
                                id = "gene", access_idx = 1){
  
  if(id=="uniprot"){
    
    idx <- which(names(progenyMembers)=="uniprot")
    progenyMembers <- progenyMembers[[idx]]
    
  } else {
    
    idx <- which(names(progenyMembers)=="gene")
    progenyMembers <- progenyMembers[[idx]]
    
  }
  
  members <- matrix(data = , nrow = 1, ncol = 2)
  pathways <- colnames(progeny)
  
  ctrl <- intersect(x = access_idx, y = 1:nrow(progeny))
  if(length(ctrl)==0){
    stop("The indeces you inserted do not correspond to 
              the number of rows/samples")
  }
  
  for(ii in 1:length(pathways)){
    
    mm <- progenyMembers[[which(names(progenyMembers)==pathways[ii])]]
    for(jj in 1:length(mm)){
      
      members <- rbind(members, c(pathways[ii], mm[jj]))
      
    }
    
  }
  
  members <- members[-1, ]
  
  scores <- matrix(data = , nrow = nrow(progeny), ncol = nrow(members))
  colnames(scores) <- members[, 2]
  rownames(scores) <- rownames(progeny)
  
  members <- unique(members)
  
  for(i in 1:ncol(scores)){
    
    for(j in 1:nrow(scores)){
      
      scores[j, i] <- 
        as.numeric(
          progeny[j, members[which(members[, 2]==colnames(scores)[i]), 1]])
      
    }
    
  }
  
  pxList <- list()
  for(ii in 1:length(access_idx)){
    pxList[[length(pxList)+1]] <- 
      as.data.frame(t(as.matrix(scores[access_idx[ii], ])))
  }
  
  names(pxList) <- rownames(progeny)[ctrl]
  
  return(pxList)

  
}