R/eigenMetabolites.R

In krumsieklab/MoDentify: Phenotype-driven module identification

#' Calculate eigenmetabolites as representatives
#'
#'
#' @param data a \code{\link[data.table]{data.table}} containing the data, where
#' columns correspond to variables and rows to observations.
#' @param group A list containing the grouping (e.g. pathways) of the variables.
#' If this is \code{NULL} all variables will be treated as they were in the same
#' group and only one representation will be calculated
#' @param method the method for calculating eigenmetabolites. Currently PCA and
#' SVD are supported.
#' @references
#' \insertRef{Langfelder2007}{MoDentify}
#' @export
#' @import data.table
#' @importFrom stats prcomp
#' @return list of two, M: \code{\link[data.table]{data.table}} of eigenscores,
#' expvar: full lists of explained variances
#' @examples
#' data(qmdiab.data)
#' data(qmdiab.annos)
#' 
#' eigen.data <- eigenMetabolites(
#'   data = qmdiab.data,
#'   group = qmdiab.annos$Sub.pathway, method = "PCA"
#' )
eigenMetabolites <- function(data, group = NULL, method = "PCA") {
  if (is.null(group)) {
    group <- rep("Group", dim(data)[2])
  }
  unique.group <- unique(group)
  if (method == "PCA") {
    res <- sapply(unique.group, function(g) {
      pca <- prcomp(as.data.table(data[, group == g]))
      list(
        pc1 = pca$x[, 1],
        expvar = (pca$sdev)^2 / sum(pca$sdev^2)
      )
    }, simplify = FALSE)
    # assemble matrix
    M <- as.data.table(sapply(res, function(x) {
      x$pc1
    }))
    # assemble expvars
    expvar <- sapply(res, function(x) {
      x$expvar
    }, simplify = FALSE)
    # return
    return(list(M = M, expvar = expvar))
  } else if (method == "SVD") {
    res <- sapply(unique.group, function(g) {
      svd <- svd(t(as.data.table(data[, group == g])))
      list(v1 = svd$v[, 1])
    }, simplify = FALSE)
    # assemble matrix
    M <- as.data.table(sapply(res, function(x) {
      x$v1
    }))
    # return
    return(list(M = M))
  }
}