R/OrderNames.R

In CoDiNA: Co-Expression Differential Network Analysis

#' @title OrderNames
#' @description Sorts each link's Nodes by the smallest value. Removes links that both nodes are the same.
#' @param M data.frame to have the names ordered. Node.1, Node.2 and correlation value.
#'
#' @return a data.table whith Node.1 and Node.2, sorted by the smallest value between both.
#' @author Deisy Morselli Gysi <deisy at bioinf.uni-leipzig.de>
#' @export
#' @importFrom data.table data.table
#' @examples
#' Nodes = LETTERS[1:10]
#' Z = data.frame(Node.1 = sample(Nodes) ,
#' Node.2 = sample(Nodes), cor = runif(10,-1,1))
#' OrderNames(Z)
#' 
OrderNames = function (M) {
  M$Node.1  %<>% as.character()
  M$Node.2  %<>% as.character()
  n1 = apply(M[, 1:2], 1, min)
  n2 = apply(M[, 1:2], 1, max)
  df = data.table::data.table(Node.1 = n1, Node.2 = n2, cor = M[, 
                                                                3])
  names(df)[3] = "cor"
  df = subset(df, df$Node.1 != df$Node.2)
  df = subset(df, !is.na(df$Node.1))
  df = subset(df, !is.na(df$Node.2))
  df = subset(df, !is.na(df$cor))
  return(df)
}