R/get.node.info.R

In kridsadakorn/ipcaps.bioc: Iterative Pruning to Capture Population Structure

#' Get the information for specified node
#'
#' @description Obtain the information for specified
#' node from the output list of \code{\link{ipcaps}}.
#'
#' @param cluster.obj A list returned from the \code{\link{ipcaps}} 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 = 'IPCAPS.BIOC')
#'
#' LABEL.file <- system.file('extdata',
#'                           'ipcaps_example_individuals.txt.gz',
#'                           package = 'IPCAPS.BIOC')
#'
#' my.cluster <- ipcaps(bed = BED.file,
#'                      label.file = LABEL.file,
#'                      lab.col = 2,
#'                      out = tempdir(),
#'                      max.thread = 1,
#'                      seed = 1234)
#'
#' #Here, to obtain the information of specified node, for example, node 3
#' node.info <- get.node.info(my.cluster,3)


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)
        }
    }
}