R/getmgsa.R

In mengchen18/mogsa: Multiple omics data integrative clustering and gene set analysis

#' get values in an object of class "mgsa".
#' 
#' get values/slot in an object of class "mgsa". The "mgsa" consists of two S4
#' class objects, \code{\link{moa-class}} and \code{\link{moa.sup-class}}. This
#' function could extract values in these two components directly.
#' 
#' if value in c("call", "moa", "sup"), the function equal function
#' \code{\link{slot}}.
#' 
#' if value in c("eig", "tau", "partial.eig", "eig.vec", "loading", "fac.scr",
#' "partial.fs", "ctr.obs", "ctr.var", "ctr.tab", "RV"), the function extact
#' corresponding value from \code{\link{moa-class}}.
#' 
#' if value in c("data", "coord.sep", "coord.comb", "score", "score.data",
#' "score.pc", "score.sep", "p.val"), the function extract value from
#' \code{\link{moa.sup-class}}.
#' 
#' @param mgsa An object of class \code{\link{mgsa-class}}.
#' @param value The name of the value want to extract from "mgsa". See detail
#' for options.
#' @return The function return the selected value in "mgsa".
#' @author Chen Meng
#' @references TBA
#' @export
#' @examples
#' 
#' 	# library(mogsa)
#' 	# loading gene expression data and supplementary data
#' 	data(NCI60_4array_supdata)
#' 	data(NCI60_4arrays)
#' 	mgsa <- mogsa(x = NCI60_4arrays, sup=NCI60_4array_supdata, nf=9,
#' 	              proc.row = "center_ssq1", w.data = "inertia", statis = TRUE)
#' 	part.eig <- getmgsa(mgsa, "partial.eig")
#' 	barplot(as.matrix(part.eig))
#' 
getmgsa <- function(mgsa, value) {
  
  if (!inherits(mgsa, "mgsa"))
    stop("the first input argument should be an object of class 'mgsa'.")
  if (value %in% c("call", "moa", "sup"))
    r <- slot(mgsa, value) else 
      if (value %in% c("eig", "tau", "partial.eig", "eig.vec", "loading", 
                       "fac.scr", "partial.fs", "ctr.obs", "ctr.var", "ctr.tab", "RV"))
        r <- slot(mgsa@moa, value) else 
          if (value %in% c("data", "coord.sep", "coord.comb", "score", 
                           "score.data", "score.pc", "score.sep", "p.val")) 
            r <- slot(mgsa@sup, value) else
              stop("unknown value selected.")
  return(r)
}