R/calculateModuleRepresentatives.R

In krumsiek/MoDentify: Phenotype-driven module identification

#' Calculate Module Representative
#'
#'
#' @param data a \code{\link[data.table]{data.table}} with three columns: name,
#' sampleID and z-score.
#' @param representative.method the method, that is used for calculation of the
#' representatives. Currently implemented:"eigenmetabolite" and "average"
#'
#' @importFrom stats prcomp
#' @import data.table
#' @references
#' \insertRef{Langfelder2007}{MoDentify}
#' @references
#' \insertRef{Chuang2007}{MoDentify}
#' @return a \code{\link[data.table]{data.table}} containing the module
#' representative for each sample
calculateModuleRepresentatives <- function(data, representative.method = "average") {
  if (representative.method == "average") {
    repdata <- data[, .(representative = mean(z.score)), by = .(sampleID)]
  } else if (representative.method == "eigenmetabolite") {
    if ("met.name" %in% colnames(data)) {
      data <- dcast(data, sampleID ~ met.name, value.var = "z.score")
    } else {
      data <- dcast(data, sampleID ~ name, value.var = "z.score")
    }
    rownames(data) <- data$sampleID
    data$sampleID <- NULL
    data <- as.data.frame(data)
    eigendata <- eigenMetabolites(data = data, method = "PCA")
    repdata <- data.table(representative = eigendata$M$Group)
  } else {
    stop("\n Method not supported.\n")
  }

  return(repdata)
}