get_link.R

#' Converts the score matrix (obtained from DPM or reg-DPM) to a sorted list of non-directed links (links with higher score first).
#'
#' @param score_matrix score matrix obtained from DPM or regDPM.
#' @param top_ranked number of top links with higher score to report. The default value is NULL, i.e. all the links are reported.
#' @param threshold only links with a score above the threshold are reported. The default value is 0, i.e. all the links are reported.
#'
#' @return List of links in a data frame. Each line of the data frame corresponds to a link. The first and second columns are the corresponding nodes of the link and the third column is the score of the link.
#'
#' @examples
#'##load DREAM4 data (insilico_size10_1_knockouts)
#' data(dream4)
#'
#'## Run regularized DPM
#' score_mat <- reg.dpm(dream4)
#'
#' ## Get ranking of links
#' links <- get_link(score_mat)
#' head(linkList)
#'
#' ## Get only the top ranked links
#' links <- get_link(score_mat,top_ranked=10)
#' head(linkList)
#'
#' ## Get only the links with a score higher than a threshold
#' links <- get_link(score_mat,threshold = 0.2)
#' head(linkList)
#'
#' @export
#'
#'
####################################################################################
### Function to converts the score matrix to a sorted list of non-directed links####
####################################################################################

get_link <- function(score_matrix, top_ranked=NULL, threshold=0) {
  diag(score_matrix) <- NA
  score_matrix[upper.tri(score_matrix)] <- NA
  linkList <- reshape2::melt(abs(score_matrix), na.rm=TRUE)
  colnames(linkList) <- c("Node1", "Node2", "score")
  linkList <- linkList[linkList$score>=threshold,]
  linkList <- linkList[order(linkList$score, decreasing=TRUE),]

  if(!is.null(top_ranked)) {
    linkList <- linkList[1:min(nrow(linkList), top_ranked),]
  }

  rownames(linkList) <- NULL

  return(linkList)
}