R/print_fun.R

In DISOhda/DiscreteFDR: FDR Based Multiple Testing Procedures with Adaptation for Discrete Tests

#' @title
#' Printing DiscreteFDR results
#' 
#' @description
#' Prints the results of discrete FDR analysis, stored in a `DiscreteFDR` class
#' object.
#' 
#' @param x      an object of class "`DiscreteFDR`".
#' @param ...    further arguments to be passed to or from other methods. They
#'               are ignored in this function.
#' 
#' @return
#' The input object `x` is invisibly returned via `invisible(x)`.
#' 
#' @template exampleGPV
#' @examples
#' DBH.su.crit <- DBH(raw.pvalues, pCDFlist, direction = "su",
#'                    ret.crit.consts = TRUE)
#' print(DBH.su.crit)
#' 
#' @importFrom stats p.adjust
#' @method print DiscreteFDR
#' @export
## S3 method for class 'DiscreteFDR'
print.DiscreteFDR <- function(x, ...){
  if(!any(c("DiscreteFDR", "summary.DiscreteFDR") %in% class(x)))
    return(print(x))
  
  n <- length(x$Data$Raw.pvalues)
  k <- x$Num.rejected
  BH <- p.adjust(x$Data$Raw.pvalues, "BH")
  
  # print title (i.e. algorithm)
  cat("\n")
  cat("\t", x$Data$Method, "\n")
  
  # print dataset name(s)
  cat("\n")
  cat("Data: ", x$Data$Data.name, "\n")
  
  # print short results overview
  if(!exists('Select', x))
    cat("Number of tests =", n, "\n") else {
      cat("Number of selected tests =", x$Select$Number, "out of", n, "\n")
      cat("Selection threshold =", x$Select$Threshold, "\n")
    }
  
  cat("Number of rejections =", k, "at global FDR level", x$Data$FDR.level,
      "\n")
  
  cont_fdr <- ifelse(grepl("Yekutieli", x$Data$Method), "BY", "BH")
  cont_adj <- p.adjust(x$Data$Raw.pvalues, cont_fdr)
  cat("(Original ", cont_fdr, " rejections = ",
      sum(cont_adj <= x$Data$FDR.level), ")\n", sep = "")
  
  if(k && !exists('Select', x)) 
    cat("Largest rejected p-value: ", max(x$Rejected), "\n")
  
  cat("\n")
  invisible(x)
}