R/AllClasses.R

In marr: Maximum rank reproducibility

#' @title the Marr class
#'
#' @description  Objects of this class store
#' needed information to work with a
#' Marr object
#'
#' @slot MarrSamplepairs Marr sample pairs
#' @slot MarrFeatures Marr features
#' @slot MarrSamplepairsfiltered Marr sample pairs post filtering
#' @slot MarrFeaturesfiltered Marr metabolites post filtering
#'
#' @return \code{MarrSamplepairs} returns the distribution of
#' percent reproducible  features (column-wise) per sample pair,
#' \code{MarrFeatures} returns the  distribution of percent reproducible
#' sample pairs (row-wise) per feature,
#' \code{MarrSamplepairsfiltered} returns the percent of reproducible
#' features based on a threshold value and
#' \code{MarrFeaturesfiltered} returns the percent of reproducible
#' sample pairs based on a threshold value
#'
#' @name Marr-class
#' @import methods
#' @exportClass Marr
#' @aliases Marr-class
#'
#' @examples
#' data <- matrix(rnorm(2400), nrow=200, ncol=12)
#' data_Marr <- Marr(object = data, pSamplepairs=0.75,
#'                   pFeatures=0.75, alpha=0.05)
#'
setClass(Class = "Marr", slot = list(MarrSamplepairs = "numeric",
            MarrFeatures = "array", MarrSamplepairsfiltered = "numeric",
            MarrFeaturesfiltered = "numeric"))
#' @param Marr
#'
#' @importFrom utils head
#' @importFrom utils tail
setMethod("show", "Marr", function(object) {
            cat("Marr: Maximum Rank reproducibility\n")
            cat("   MarrSamplepairs (length =", length(object@MarrSamplepairs),
                        "):", "\n")
            cat(c(head(round(object@MarrSamplepairs, 3), n = 3),
                        "...", tail(round(object@MarrSamplepairs, 3),
                                    n = 3)), "\n")
            cat("   MarrFeatures (length =", length(object@MarrFeatures),
                        "):", "\n")
            cat(c(head(round(object@MarrFeatures, 3), n = 3),
                        "...", tail(round(object@MarrFeatures, 3),
                                    n = 3)), "\n")
})