R/generateNetwork.R

In krumsieklab/MoDentify: Phenotype-driven module identification

#' Network inference with Gaussian graphical models (GGMs) or Pearson correlation
#'
#'
#' @param data a \code{\link[data.table]{data.table}} or matrix containing the data.
#' The columns correspond to the variables (e.g. metabolites), the rows to the observations.
#' @param covars a \code{\link[data.table]{data.table}} containing covariates to correct for.
#' The columns correspond to the different covariates, the rows to the observations.
#' @param annotations a \code{\link[data.table]{data.table}} containing annotations for the variables (e.g. pathway annotations).
#' The columns correspond to the different annotations, the rows to the variables
#' @param correlation.type type of correlation to be estimated. Can either be "pearson", or "partial".
#' @param alpha significance level (type 1 error) for multiple testing correction.
#' @param correction.method the method that should be used for multiple testing correction ("bonferroni", "BH", "BY", "fdr", "holm", "hochberg", "hommel", "none").
#' Default is bonferroni. See \code{\link[stats]{p.adjust}}.
#' @import GeneNet
#' @import data.table
#' @import igraph
#' @importFrom Hmisc rcorr
#' @importFrom stats complete.cases
#' @importFrom stats p.adjust
#' @export
#' @examples
#' data(qmdiab.data)
#' data(qmdiab.annos)
#' 
#' net.graph <- generateNetwork(
#'   data = qmdiab.data, annotations = qmdiab.annos,
#'   alpha = 0.05, correction.method = "bonferroni"
#' )
#' @return a network containing the variables as nodes as an \code{\link[igraph]{igraph}} object.
#' @references
#' \insertRef{Krumsiek2011}{MoDentify}

generateNetwork <- function(data, covars = NULL, annotations, correlation.type = "partial", alpha = 0.05,
                            correction.method = "bonferroni") {


  # warning that there are missing values and that only complete cases are taken
  if (sum(is.na(data)) > 0) {
    warning("Data matrix contains missing values.\n Only complete cases were used for network inference.\n")
  }

  # calculating Pearson correlation
  C_pear <- rcorr(as.matrix(data), type = "pearson")
  colnames(C_pear$P) <- seq_len(dim(C_pear$P)[1])
  rownames(C_pear$P) <- seq_len(dim(C_pear$P)[1])

  pearp <- C_pear$P
  pearp[lower.tri(pearp, diag = TRUE)] <- NA

  net_DT <- data.table(node1 = as.integer(rownames(pearp)), pearp)
  net_DT <- melt(net_DT, id.vars = "node1", variable.name = "node2", value.name = "p")
  net_DT[, node2 := as.integer(node2)]
  net_DT[, pearp.adjust := p.adjust(p, method = correction.method, n = choose(dim(data)[2], 2))]

  # partial correlation (GGM) or only Pearson correlation
  if (correlation.type == "partial") {


    # combining data and covariates
    if (!is.null(covars)) {
      mat <- cbind(data, covars)
    } else {
      mat <- as.matrix(data)
    }
    mat <- as.matrix(mat[complete.cases(mat), ])

    ggm <- ggm.estimate.pcor(mat, method = "static")
    ggm <- ggm[seq_len(dim(data)[2]), seq_len(dim(data)[2])]
    ggm_pvals <- as.data.table(network.test.edges(ggm, direct = FALSE, fdr = TRUE, plot = FALSE))
    ggm_pvals[, c("qval", "prob") := NULL]

    # only get complete cases
    net_DT <- net_DT[complete.cases(net_DT)]

    net_DT <- net_DT[ggm_pvals, on = c("node1", "node2")]

    net_DT$p <- net_DT$pval
    net_DT[, pval.adjust := p.adjust(pval, method = correction.method, n = choose(dim(data)[2], 2))]
    names(net_DT)[5] <- "cor"
    net_DT[, "pval" := NULL]
  } else if (correlation.type == "pearson") {
    C_pear_DT <- data.table(node1 = as.integer(rownames(C_pear$P)), C_pear$r)
    colnames(C_pear_DT) <- c("node1", colnames(C_pear$P))
    C_pear_DT <- melt(C_pear_DT, id.vars = "node1", variable.name = "node2", value.name = "cor")
    C_pear_DT[, node2 := as.integer(node2)]


    net_DT <- net_DT[C_pear_DT, on = c("node1", "node2")]
    net_DT$pval.adjust <- rep(0, dim(net_DT)[1])
    # only get complete cases
    net_DT <- net_DT[complete.cases(net_DT)]
  }

  # assigning variable labels
  net_DT[, from := colnames(C_pear$r)[node1]]
  net_DT[, to := colnames(C_pear$r)[node2]]

  # in annotations?
  net_DT <- net_DT[to %in% annotations$name & from %in% annotations$name]

  # significance filtering
  net_DT <- net_DT[pval.adjust <= alpha & pearp.adjust <= alpha]


  net_DT[, c("node1", "node2", "pearp.adjust", "pval.adjust") := NULL]
  setcolorder(net_DT, c("from", "to", "cor", "p"))



  if ("Labels" %in% colnames(annotations)) {
    annotations[, label := Labels]
  }

  if (!"label" %in% colnames(annotations)) {
    annotations$label <- annotations$name
  }

  # make sure that column name is first column in annotations
  tmpnames <- annotations$name
  annotations$name <- NULL
  annotations <- cbind(name = tmpnames, annotations)

  net_graph <- graph_from_data_frame(d = net_DT, directed = FALSE, vertices = annotations)

  return(net_graph)
}