R/get.node.info.R

In kridsadakorn/ipcaps2: Iterative Pruning to Capture Population Structure version 2

#' Get the information for specified node
#'
#' @description Obtain the information for specified
#' node from the output list of \code{\link{ipcaps2}}.
#'
#' @param cluster.obj A list returned from the \code{\link{ipcaps2}} function.
#' @param node An integer representing a node number to enquire information as
#' shown in the HTML output files.
#'
#' @return The return value is \code{NULL} if node's information does not exist or a list containing
#' \code{PCs}, \code{eigen.fit}, \code{index}, and \code{label} as explained
#' below:
#' \itemize{
#' \item \code{$PCs} is a matrix of pricipal components of this node.
#' \item \code{$eigen.fit} is a number represeting the EigenFit value of this
#' node.
#' \item \code{$index} is a vector of row number (individuals) of \code{raw.data} (input data).
#' \item \code{$label} is the vector of labels of all individuals that belongs
#' to this node.
#' }
#'
#' @export
#'
#' @examples
#'
#' # Importantly, bed file, bim file, and fam file are required
#' # Use the example files embedded in the package
#'
#' BED.file <- system.file("extdata","ipcaps_example.bed",package="IPCAPS2")
#' LABEL.file <- system.file("extdata","ipcaps_example_individuals.txt.gz",package="IPCAPS2")
#'
#' my.cluster <- ipcaps2(bed=BED.file,
#'                       label.file=LABEL.file,
#'                       lab.col=2,
#'                       out=tempdir(),
#'                       silence=TRUE,
#'                       no.rep=1)
#'
#' #Here, to obtain the information of specified node, for example, node 3
#' node.info <- get.node.info(my.cluster,3)
#' ls(node.info)

get.node.info <- function(cluster.obj, node)
{
  PCs <- NULL
  eigen.fit <- NULL

  index <- NULL
  label <- NULL

  if (is.null(cluster.obj$output.dir))
  {
    cat(
      paste0(
        "Incorrect parameter, please use the object returned from the ",
        "function ipcaps as an input\n"
      )
    )
    return(NULL)
  } else
  {
    file.name <-
      file.path(cluster.obj$output.dir,
                "RData",
                paste0("node",
                       node, ".RData"))
    if (!file.exists(file.name))
    {
      cat(paste0("Node ", node, " doesn't exist\n"))
      return(NULL)
    } else
    {
      load(file.name)
      res <- list(
        PCs = PCs,
        eigen.fit = eigen.fit,
        index = index,
        label = label
      )
      return(res)
    }
  }
}