R/print_data_objects.R

In pmartR/pmartR: Panomics Marketplace - Quality Control and Statistical Analysis for Panomics Data

#' print.pepData
#'
#' For printing an S3 object of type 'pepData'
#' @param x An object of type 'pepData'
#' @param ...  further arguments passed to or from other methods
#'
#' @return No return value, prints details about x
#' 
#' @rdname print-pepData
#' @export
#'
print.pepData <- function(x, ...) {
  pepData <- x

  # Make sure we only have valid arguments
  if (length(list(...)) > 0) {
    warning("unused argument(s): ",
             toString(as.list(tail(match.call(), length(list(...))))))
  }
  
  if (!inherits(pepData, "pepData")) stop("pep_object must be of the class 'pepData'")

  e_data <- as.data.frame(lapply(pepData$e_data, as.character), stringsAsFactors = FALSE, check.names = FALSE)
  f_data <- as.data.frame(lapply(pepData$f_data, as.character), stringsAsFactors = FALSE, check.names = FALSE)
  edata_ncols <- ncol(e_data)
  fdata_ncols <- ncol(f_data)
  blank_row = rep("----", 5)

  if (!is.null(pepData$e_meta)) {
    e_meta <- as.data.frame(lapply(pepData$e_meta, as.character), stringsAsFactors = FALSE, check.names = FALSE)
    emeta_ncols <- ncol(e_meta)

    if (nrow(e_data) >= 9) {
      e_data_head = head(e_data, 4)[, 1:min(edata_ncols, 5)]
      e_data_tail = tail(e_data, 4)[, 1:min(edata_ncols, 5)]
      edata = rbind(e_data_head, blank_row, e_data_tail)
    } else {
      edata = e_data
    }

    if (nrow(f_data) >= 9) {
      f_data_head = head(f_data, 4)[, 1:min(fdata_ncols, 5)]
      f_data_tail = tail(f_data, 4)[, 1:min(fdata_ncols, 5)]
      fdata = rbind(f_data_head, blank_row, f_data_tail)
    } else {
      fdata = f_data
    }

    if (nrow(e_meta) >= 9) {
      e_meta_head = head(e_meta, 4)[, 1:min(emeta_ncols, 5)]
      e_meta_tail = tail(e_meta, 4)[, 1:min(emeta_ncols, 5)]
      emeta = rbind(e_meta_head, blank_row, e_meta_tail)
    } else {
      emeta = e_meta
    }

    if (edata_ncols > 5) message("only first 5 columns are shown")
    cat("e_data\n")
    cat(capture.output(edata), sep = "\n")
    cat("\n")

    if (fdata_ncols > 5) message("only first 5 columns are shown")
    cat("f_data\n")
    cat(capture.output(fdata), sep = "\n")
    cat("\n")

    if (emeta_ncols > 5) message("only first 5 columns are shown")
    cat("e_meta\n")
    cat(capture.output(emeta), sep = "\n")
    cat("\n")
  } else {
    if (nrow(e_data) >= 9) {
      e_data_head = head(e_data, 4)[, 1:min(edata_ncols, 5)]
      e_data_tail = tail(e_data, 4)[, 1:min(edata_ncols, 5)]
      edata = rbind(e_data_head, blank_row, e_data_tail)
    } else {
      edata = e_data
    }

    if (nrow(f_data) >= 9) {
      f_data_head = head(f_data, 4)[, 1:min(fdata_ncols, 5)]
      f_data_tail = tail(f_data, 4)[, 1:min(fdata_ncols, 5)]
      fdata = rbind(f_data_head, blank_row, f_data_tail)
    } else {
      fdata = f_data
    }

    if (edata_ncols > 5) message("only first 5 columns are shown")
    cat("e_data\n")
    cat(capture.output(edata), sep = "\n")
    cat("\n")

    if (fdata_ncols > 5) message("only first 5 columns are shown")
    cat("f_data\n")
    cat(capture.output(fdata), sep = "\n")
    cat("\n")
  }
}

#' print.metabData
#'
#' For printing an S3 object of type 'metabData'
#' @param x An object of type 'metabData'
#' @param ...  further arguments passed to or from other methods
#'
#' @return No return value, prints details about x
#' 
#' @rdname print-metabData
#' @export
#'
print.metabData <- function(x, ...) {
  metabData <- x

  # Make sure we only have valid arguments
  if (length(list(...)) > 0) {
    warning("unused argument(s): ",
             toString(as.list(tail(match.call(), length(list(...))))))
  }
  
  if (!inherits(metabData, "metabData")) stop("metab_object must be of the class 'metabData'")

  e_data <- as.data.frame(lapply(metabData$e_data, as.character), stringsAsFactors = FALSE, check.names = FALSE)
  f_data <- as.data.frame(lapply(metabData$f_data, as.character), stringsAsFactors = FALSE, check.names = FALSE)
  edata_ncols <- ncol(e_data)
  fdata_ncols <- ncol(f_data)
  blank_row = rep("----", 5)

  if (!is.null(metabData$e_meta)) {
    e_meta <- as.data.frame(lapply(metabData$e_meta, as.character), stringsAsFactors = FALSE, check.names = FALSE)
    emeta_ncols <- ncol(e_meta)

    if (nrow(e_data) >= 9) {
      e_data_head = head(e_data, 4)[, 1:min(edata_ncols, 5)]
      e_data_tail = tail(e_data, 4)[, 1:min(edata_ncols, 5)]
      edata = rbind(e_data_head, blank_row, e_data_tail)
    } else {
      edata = e_data
    }

    if (nrow(f_data) >= 9) {
      f_data_head = head(f_data, 4)[, 1:min(fdata_ncols, 5)]
      f_data_tail = tail(f_data, 4)[, 1:min(fdata_ncols, 5)]
      fdata = rbind(f_data_head, blank_row, f_data_tail)
    } else {
      fdata = f_data
    }

    if (nrow(e_meta) >= 9) {
      e_meta_head = head(e_meta, 4)[, 1:min(emeta_ncols, 5)]
      e_meta_tail = tail(e_meta, 4)[, 1:min(emeta_ncols, 5)]
      emeta = rbind(e_meta_head, blank_row, e_meta_tail)
    } else {
      emeta = e_meta
    }

    if (edata_ncols > 5) message("only first 5 columns are shown")
    cat("e_data\n")
    cat(capture.output(edata), sep = "\n")
    cat("\n")

    if (fdata_ncols > 5) message("only first 5 columns are shown")
    cat("f_data\n")
    cat(capture.output(fdata), sep = "\n")
    cat("\n")

    if (emeta_ncols > 5) message("only first 5 columns are shown")
    cat("e_meta\n")
    cat(capture.output(emeta), sep = "\n")
    cat("\n")
  } else {
    if (nrow(e_data) >= 9) {
      e_data_head = head(e_data, 4)[, 1:min(edata_ncols, 5)]
      e_data_tail = tail(e_data, 4)[, 1:min(edata_ncols, 5)]
      edata = rbind(e_data_head, blank_row, e_data_tail)
    } else {
      edata = e_data
    }

    if (nrow(f_data) >= 9) {
      f_data_head = head(f_data, 4)[, 1:min(fdata_ncols, 5)]
      f_data_tail = tail(f_data, 4)[, 1:min(fdata_ncols, 5)]
      fdata = rbind(f_data_head, blank_row, f_data_tail)
    } else {
      fdata = f_data
    }

    if (edata_ncols > 5) message("only first 5 columns are shown")
    cat("e_data\n")
    cat(capture.output(edata), sep = "\n")
    cat("\n")

    if (fdata_ncols > 5) message("only first 5 columns are shown")
    cat("f_data\n")
    cat(capture.output(fdata), sep = "\n")
    cat("\n")
  }
}

#' print.proData
#'
#' For printing an S3 object of type 'proData'
#' @param x An object of type 'proData'
#' @param ...  further arguments passed to or from other methods
#'
#' @return No return value, prints details about x
#' 
#' @rdname print-proData
#' @export
#'
print.proData <- function(x, ...) {
  proData <- x

  # Make sure we only have valid arguments
  if (length(list(...)) > 0) {
    warning("unused argument(s): ",
             toString(as.list(tail(match.call(), length(list(...))))))
  }
  
  if (!inherits(proData, "proData")) stop("pro_object must be of the class 'proData'")

  e_data <- as.data.frame(lapply(proData$e_data, as.character), stringsAsFactors = FALSE, check.names = FALSE)
  f_data <- as.data.frame(lapply(proData$f_data, as.character), stringsAsFactors = FALSE, check.names = FALSE)
  edata_ncols <- ncol(e_data)
  fdata_ncols <- ncol(f_data)
  blank_row = rep("----", 5)

  if (!is.null(proData$e_meta)) {
    e_meta <- as.data.frame(lapply(proData$e_meta, as.character), stringsAsFactors = FALSE, check.names = FALSE)
    emeta_ncols <- ncol(e_meta)

    if (nrow(e_data) >= 9) {
      e_data_head = head(e_data, 4)[, 1:min(edata_ncols, 5)]
      e_data_tail = tail(e_data, 4)[, 1:min(edata_ncols, 5)]
      edata = rbind(e_data_head, blank_row, e_data_tail)
    } else {
      edata = e_data
    }

    if (nrow(f_data) >= 9) {
      f_data_head = head(f_data, 4)[, 1:min(fdata_ncols, 5)]
      f_data_tail = tail(f_data, 4)[, 1:min(fdata_ncols, 5)]
      fdata = rbind(f_data_head, blank_row, f_data_tail)
    } else {
      fdata = f_data
    }

    if (nrow(e_meta) >= 9) {
      e_meta_head = head(e_meta, 4)[, 1:min(emeta_ncols, 5)]
      e_meta_tail = tail(e_meta, 4)[, 1:min(emeta_ncols, 5)]
      emeta = rbind(e_meta_head, blank_row, e_meta_tail)
    } else {
      emeta = e_meta
    }

    if (edata_ncols > 5) message("only first 5 columns are shown")
    cat("e_data\n")
    cat(capture.output(edata), sep = "\n")
    cat("\n")

    if (fdata_ncols > 5) message("only first 5 columns are shown")
    cat("f_data\n")
    cat(capture.output(fdata), sep = "\n")
    cat("\n")

    if (emeta_ncols > 5) message("only first 5 columns are shown")
    cat("e_meta\n")
    cat(capture.output(emeta), sep = "\n")
    cat("\n")
  } else {
    if (nrow(e_data) >= 9) {
      e_data_head = head(e_data, 4)[, 1:min(edata_ncols, 5)]
      e_data_tail = tail(e_data, 4)[, 1:min(edata_ncols, 5)]
      edata = rbind(e_data_head, blank_row, e_data_tail)
    } else {
      edata = e_data
    }

    if (nrow(f_data) >= 9) {
      f_data_head = head(f_data, 4)[, 1:min(fdata_ncols, 5)]
      f_data_tail = tail(f_data, 4)[, 1:min(fdata_ncols, 5)]
      fdata = rbind(f_data_head, blank_row, f_data_tail)
    } else {
      fdata = f_data
    }

    if (edata_ncols > 5) message("only first 5 columns are shown")
    cat("e_data\n")
    cat(capture.output(edata), sep = "\n")
    cat("\n")

    if (fdata_ncols > 5) message("only first 5 columns are shown")
    cat("f_data\n")
    cat(capture.output(fdata), sep = "\n")
    cat("\n")
  }
}

#' print.lipidData
#'
#' For printing an S3 object of type 'lipidData'
#' @param x An object of type 'lipidData'
#' @param ...  further arguments passed to or from other methods
#'
#' @return No return value, prints details about x
#'
#' @rdname print-lipidData
#' @export
#'
print.lipidData <- function(x, ...) {
  lipidData <- x

  # Make sure we only have valid arguments
  if (length(list(...)) > 0) {
    warning("unused argument(s): ",
             toString(as.list(tail(match.call(), length(list(...))))))
  }
  
  if (!inherits(lipidData, "lipidData")) stop("lipid_object must be of the class 'lipidData'")

  e_data <- as.data.frame(lapply(lipidData$e_data, as.character), stringsAsFactors = FALSE, check.names = FALSE)
  f_data <- as.data.frame(lapply(lipidData$f_data, as.character), stringsAsFactors = FALSE, check.names = FALSE)
  edata_ncols <- ncol(e_data)
  fdata_ncols <- ncol(f_data)
  blank_row = rep("----", 5)

  if (!is.null(lipidData$e_meta)) {
    e_meta <- as.data.frame(lapply(lipidData$e_meta, as.character), stringsAsFactors = FALSE, check.names = FALSE)
    emeta_ncols <- ncol(e_meta)

    if (nrow(e_data) >= 9) {
      e_data_head = head(e_data, 4)[, 1:min(edata_ncols, 5)]
      e_data_tail = tail(e_data, 4)[, 1:min(edata_ncols, 5)]
      edata = rbind(e_data_head, blank_row, e_data_tail)
    } else {
      edata = e_data
    }

    if (nrow(f_data) >= 9) {
      f_data_head = head(f_data, 4)[, 1:min(fdata_ncols, 5)]
      f_data_tail = tail(f_data, 4)[, 1:min(fdata_ncols, 5)]
      fdata = rbind(f_data_head, blank_row, f_data_tail)
    } else {
      fdata = f_data
    }

    if (nrow(e_meta) >= 9) {
      e_meta_head = head(e_meta, 4)[, 1:min(emeta_ncols, 5)]
      e_meta_tail = tail(e_meta, 4)[, 1:min(emeta_ncols, 5)]
      emeta = rbind(e_meta_head, blank_row, e_meta_tail)
    } else {
      emeta = e_meta
    }

    if (edata_ncols > 5) message("only first 5 columns are shown")
    cat("e_data\n")
    cat(capture.output(edata), sep = "\n")
    cat("\n")

    if (fdata_ncols > 5) message("only first 5 columns are shown")
    cat("f_data\n")
    cat(capture.output(fdata), sep = "\n")
    cat("\n")

    if (emeta_ncols > 5) message("only first 5 columns are shown")
    cat("e_meta\n")
    cat(capture.output(emeta), sep = "\n")
    cat("\n")
  } else {
    if (nrow(e_data) >= 9) {
      e_data_head = head(e_data, 4)[, 1:min(edata_ncols, 5)]
      e_data_tail = tail(e_data, 4)[, 1:min(edata_ncols, 5)]
      edata = rbind(e_data_head, blank_row, e_data_tail)
    } else {
      edata = e_data
    }

    if (nrow(f_data) >= 9) {
      f_data_head = head(f_data, 4)[, 1:min(fdata_ncols, 5)]
      f_data_tail = tail(f_data, 4)[, 1:min(fdata_ncols, 5)]
      fdata = rbind(f_data_head, blank_row, f_data_tail)
    } else {
      fdata = f_data
    }

    if (edata_ncols > 5) message("only first 5 columns are shown")
    cat("e_data\n")
    cat(capture.output(edata), sep = "\n")
    cat("\n")

    if (fdata_ncols > 5) message("only first 5 columns are shown")
    cat("f_data\n")
    cat(capture.output(fdata), sep = "\n")
    cat("\n")
  }
}

#' print.seqData
#'
#' For printing an S3 object of type 'seqData'
#' @param x An object of type 'seqData'
#' @param ...  further arguments passed to or from other methods
#'
#' @return No return value, prints details about x
#' 
#' @rdname print-seqData
#' @export
#'
print.seqData <- function(x, ...) {
  seqData <- x

  # Make sure we only have valid arguments
  if (length(list(...)) > 0) {
    warning("unused argument(s): ",
             toString(as.list(tail(match.call(), length(list(...))))))
  }
  
  if (!inherits(seqData, "seqData")) stop("lipid_object must be of the class 'seqData'")

  e_data <- as.data.frame(lapply(seqData$e_data, as.character), stringsAsFactors = FALSE, check.names = FALSE)
  f_data <- as.data.frame(lapply(seqData$f_data, as.character), stringsAsFactors = FALSE, check.names = FALSE)
  edata_ncols <- ncol(e_data)
  fdata_ncols <- ncol(f_data)
  blank_row = rep("----", 5)

  if (!is.null(seqData$e_meta)) {
    e_meta <- as.data.frame(lapply(seqData$e_meta, as.character), stringsAsFactors = FALSE, check.names = FALSE)
    emeta_ncols <- ncol(e_meta)

    if (nrow(e_data) >= 9) {
      e_data_head = head(e_data, 4)[, 1:min(edata_ncols, 5)]
      e_data_tail = tail(e_data, 4)[, 1:min(edata_ncols, 5)]
      edata = rbind(e_data_head, blank_row, e_data_tail)
    } else {
      edata = e_data
    }

    if (nrow(f_data) >= 9) {
      f_data_head = head(f_data, 4)[, 1:min(fdata_ncols, 5)]
      f_data_tail = tail(f_data, 4)[, 1:min(fdata_ncols, 5)]
      fdata = rbind(f_data_head, blank_row, f_data_tail)
    } else {
      fdata = f_data
    }

    if (nrow(e_meta) >= 9) {
      e_meta_head = head(e_meta, 4)[, 1:min(emeta_ncols, 5)]
      e_meta_tail = tail(e_meta, 4)[, 1:min(emeta_ncols, 5)]
      emeta = rbind(e_meta_head, blank_row, e_meta_tail)
    } else {
      emeta = e_meta
    }

    if (edata_ncols > 5) message("only first 5 columns are shown")
    cat("e_data\n")
    cat(capture.output(edata), sep = "\n")
    cat("\n")

    if (fdata_ncols > 5) message("only first 5 columns are shown")
    cat("f_data\n")
    cat(capture.output(fdata), sep = "\n")
    cat("\n")

    if (emeta_ncols > 5) message("only first 5 columns are shown")
    cat("e_meta\n")
    cat(capture.output(emeta), sep = "\n")
    cat("\n")
  } else {
    if (nrow(e_data) >= 9) {
      e_data_head = head(e_data, 4)[, 1:min(edata_ncols, 5)]
      e_data_tail = tail(e_data, 4)[, 1:min(edata_ncols, 5)]
      edata = rbind(e_data_head, blank_row, e_data_tail)
    } else {
      edata = e_data
    }

    if (nrow(f_data) >= 9) {
      f_data_head = head(f_data, 4)[, 1:min(fdata_ncols, 5)]
      f_data_tail = tail(f_data, 4)[, 1:min(fdata_ncols, 5)]
      fdata = rbind(f_data_head, blank_row, f_data_tail)
    } else {
      fdata = f_data
    }

    if (edata_ncols > 5) message("only first 5 columns are shown")
    cat("e_data\n")
    cat(capture.output(edata), sep = "\n")
    cat("\n")

    if (fdata_ncols > 5) message("only first 5 columns are shown")
    cat("f_data\n")
    cat(capture.output(fdata), sep = "\n")
    cat("\n")
  }
}


#' print.dataRes
#'
#' For printing an S3 object of class 'dataRes'
#' @param x An object of class 'dataRes'
#' @param ...  further arguments passed to or from other methods
#'
#' @return No return value, prints details about x.
#'
#' @rdname print-dataRes
#' @export
#'
print.dataRes <- function(x, ...) {
  dataRes <- x

  # Make sure we only have valid arguments
  if (length(list(...)) > 0) {
    warning("unused argument(s): ",
             toString(as.list(tail(match.call(), length(list(...))))))
  }
  
  if ((!is.null(attr(dataRes, "groupvar")) & attr(dataRes, "by") == "molecule") | (is.null(attr(dataRes, "groupvar")) & !is.null(attr(dataRes, "group_DF")) & (attr(dataRes, "by") == "molecule"))) {
    # extract item from dataRes, n_per_grp
    n_per_grp <- as.data.frame(lapply(dataRes$n_per_grp, as.character), stringsAsFactors = FALSE)

    # choosing how many rows to print
    if (nrow(n_per_grp) <= 10) {
      cat("n_per_grp\n")
      print(n_per_grp)
    } else {
      head_n_per_grp = head(n_per_grp, 5)[, 1:min(ncol(n_per_grp), 5)]
      tail_n_per_grp = tail(n_per_grp, 5)[, 1:min(ncol(n_per_grp), 5)]
      blank_row = rep("----", min(ncol(n_per_grp), 5))

      print_n_per_grp <- rbind(head_n_per_grp, blank_row, tail_n_per_grp)

      if (ncol(n_per_grp) > 5) message("only first 5 columns are shown")
      cat("n_per_grp\n")
      cat(capture.output(print_n_per_grp), sep = "\n")
      cat("\n")
    }

    # extract item from dataRes, mean
    mean <- as.data.frame(lapply(dataRes$mean, as.character), stringsAsFactors = FALSE)

    # choosing how many rows to print
    if (nrow(mean) <= 10) {
      print(mean)
    } else {
      head_mean = head(mean, 5)[, 1:min(ncol(mean), 5)]
      tail_mean = tail(mean, 5)[, 1:min(ncol(mean), 5)]
      blank_row = rep("----", min(ncol(mean), 5))

      print_mean <- rbind(head_mean, blank_row, tail_mean)

      if (ncol(mean) > 5) message("only first 5 columns are shown")
      cat("mean\n")
      cat(capture.output(print_mean), sep = "\n")
      cat("\n")
    }

    # extract item from dataRes, std_dev
    sd <- as.data.frame(lapply(dataRes$sd, as.character), stringsAsFactors = FALSE)

    # choosing how many rows to print
    if (nrow(sd) <= 10) {
      print(sd)
    } else {
      head_sd = head(sd, 5)[, 1:min(ncol(sd), 5)]
      tail_sd = tail(sd, 5)[, 1:min(ncol(sd), 5)]
      blank_row = rep("----", min(ncol(sd), 5))

      print_sd <- rbind(head_sd, blank_row, tail_sd)

      if (ncol(sd) > 5) message("only first 5 columns are shown")
      cat("std_dev\n")
      cat(capture.output(print_sd), sep = "\n")
      cat("\n")
    }

    # extract item from dataRes, median
    median <- as.data.frame(lapply(dataRes$median, as.character), stringsAsFactors = FALSE)

    # choosing how many rows to print
    if (nrow(median) <= 10) {
      print(median)
    } else {
      head_median = head(median, 5)[, 1:min(ncol(median), 5)]
      tail_median = tail(median, 5)[, 1:min(ncol(median), 5)]
      blank_row = rep("----", min(ncol(median), 5))

      print_median <- rbind(head_median, blank_row, tail_median)

      if (ncol(median) > 5) message("only first 5 columns are shown")
      cat("median\n")
      cat(capture.output(print_median), sep = "\n")
      cat("\n")
    }

    # extract item from dataRes, pct_obs
    pct_obs <- as.data.frame(lapply(dataRes$pct_obs, as.character), stringsAsFactors = FALSE)

    # choosing how many rows to print
    if (nrow(pct_obs) <= 10) {
      print(pct_obs)
    } else {
      head_pct_obs = head(pct_obs, 5)[, 1:min(ncol(pct_obs), 5)]
      tail_pct_obs = tail(pct_obs, 5)[, 1:min(ncol(pct_obs), 5)]
      blank_row = rep("----", min(ncol(pct_obs), 5))

      print_pct_obs <- rbind(head_pct_obs, blank_row, tail_pct_obs)

      if (ncol(pct_obs) > 5) message("only first 5 columns are shown")
      cat("pct_obs\n")
      cat(capture.output(print_pct_obs), sep = "\n")
      cat("\n")
    }

    # extract item from dataRes, min
    min <- as.data.frame(lapply(dataRes$min, as.character), stringsAsFactors = FALSE)

    # choosing how many rows to print
    if (nrow(min) <= 10) {
      print(min)
    } else {
      head_min = head(min, 5)[, 1:min(ncol(min), 5)]
      tail_min = tail(min, 5)[, 1:min(ncol(min), 5)]
      blank_row = rep("----", min(ncol(min), 5))

      print_min <- rbind(head_min, blank_row, tail_min)

      if (ncol(min) > 5) message("only first 5 columns are shown")
      cat("minimum\n")
      cat(capture.output(print_min), sep = "\n")
      cat("\n")
    }

    # extract item from dataRes, max
    max <- as.data.frame(lapply(dataRes$max, as.character), stringsAsFactors = FALSE)

    # choosing how many rows to print
    if (nrow(max) <= 10) {
      print(max)
    } else {
      head_max = head(max, 5)[, 1:min(ncol(max), 5)]
      tail_max = tail(max, 5)[, 1:min(ncol(max), 5)]
      blank_row = rep("----", min(ncol(max), 5))

      print_max <- rbind(head_max, blank_row, tail_max)

      if (ncol(max) > 5) message("only first 5 columns are shown")
      cat("maximum\n")
      cat(capture.output(print_max), sep = "\n")
      cat("\n")
    }
  } else {
    # extract item from dataRes, mean
    mean <- as.data.frame(lapply(dataRes$mean, as.character), stringsAsFactors = FALSE)

    # choosing how many rows to print
    if (nrow(mean) <= 10) {
      print(mean)
    } else {
      head_mean = head(mean, 5)[, 1:min(ncol(mean), 5)]
      tail_mean = tail(mean, 5)[, 1:min(ncol(mean), 5)]
      blank_row = rep("----", min(ncol(mean), 5))

      print_mean <- rbind(head_mean, blank_row, tail_mean)

      if (ncol(mean) > 5) message("only first 5 columns are shown")
      cat("mean\n")
      cat(capture.output(print_mean), sep = "\n")
      cat("\n")
    }

    # extract item from dataRes, std_dev
    sd <- as.data.frame(lapply(dataRes$sd, as.character), stringsAsFactors = FALSE)

    # choosing how many rows to print
    if (nrow(sd) <= 10) {
      print(sd)
    } else {
      head_sd = head(sd, 5)[, 1:min(ncol(sd), 5)]
      tail_sd = tail(sd, 5)[, 1:min(ncol(sd), 5)]
      blank_row = rep("----", min(ncol(sd), 5))

      print_sd <- rbind(head_sd, blank_row, tail_sd)

      if (ncol(sd) > 5) message("only first 5 columns are shown")
      cat("std_dev\n")
      cat(capture.output(print_sd), sep = "\n")
      cat("\n")
    }

    # extract item from dataRes, median
    median <- as.data.frame(lapply(dataRes$median, as.character), stringsAsFactors = FALSE)

    # choosing how many rows to print
    if (nrow(median) <= 10) {
      print(median)
    } else {
      head_median = head(median, 5)[, 1:min(ncol(median), 5)]
      tail_median = tail(median, 5)[, 1:min(ncol(median), 5)]
      blank_row = rep("----", min(ncol(median), 5))

      print_median <- rbind(head_median, blank_row, tail_median)

      if (ncol(median) > 5) message("only first 5 columns are shown")
      cat("median\n")
      cat(capture.output(print_median), sep = "\n")
      cat("\n")
    }

    # extract item from dataRes, pct_obs
    pct_obs <- as.data.frame(lapply(dataRes$pct_obs, as.character), stringsAsFactors = FALSE)

    # choosing how many rows to print
    if (nrow(pct_obs) <= 10) {
      print(pct_obs)
    } else {
      head_pct_obs = head(pct_obs, 5)[, 1:min(ncol(pct_obs), 5)]
      tail_pct_obs = tail(pct_obs, 5)[, 1:min(ncol(pct_obs), 5)]
      blank_row = rep("----", min(ncol(pct_obs), 5))

      print_pct_obs <- rbind(head_pct_obs, blank_row, tail_pct_obs)

      if (ncol(pct_obs) > 5) message("only first 5 columns are shown")
      cat("pct_obs\n")
      cat(capture.output(print_pct_obs), sep = "\n")
      cat("\n")
    }

    # extract item from dataRes, min
    min <- as.data.frame(lapply(dataRes$min, as.character), stringsAsFactors = FALSE)

    # choosing how many rows to print
    if (nrow(min) <= 10) {
      print(min)
    } else {
      head_min = head(min, 5)[, 1:min(ncol(min), 5)]
      tail_min = tail(min, 5)[, 1:min(ncol(min), 5)]
      blank_row = rep("----", min(ncol(min), 5))

      print_min <- rbind(head_min, blank_row, tail_min)

      if (ncol(min) > 5) message("only first 5 columns are shown")
      cat("minimum\n")
      cat(capture.output(print_min), sep = "\n")
      cat("\n")
    }

    # extract item from dataRes, max
    max <- as.data.frame(lapply(dataRes$max, as.character), stringsAsFactors = FALSE)

    # choosing how many rows to print
    if (nrow(max) <= 10) {
      print(max)
    } else {
      head_max = head(max, 5)[, 1:min(ncol(max), 5)]
      tail_max = tail(max, 5)[, 1:min(ncol(max), 5)]
      blank_row = rep("----", min(ncol(max), 5))

      print_max <- rbind(head_max, blank_row, tail_max)

      if (ncol(max) > 5) message("only first 5 columns are shown")
      cat("maximum\n")
      cat(capture.output(print_max), sep = "\n")
      cat("\n")
    }
  }
}



#' print.normRes
#'
#' For printing an S3 object of type 'normRes'
#' @param x An object of type 'normRes'
#' @param ...  further arguments passed to or from other methods
#'
#' @return No return value, prints details about x
#' 
#' @rdname print-normRes
#' @export
#'
print.normRes <- function(x, ...) {
  normRes <- x

  # Make sure we only have valid arguments
  if (length(list(...)) > 0) {
    warning("unused argument(s): ",
             toString(as.list(tail(match.call(), length(list(...))))))
  }
  
  attr(normRes, "class") <- NULL
  attr(normRes, "omicsData") <- NULL

  print(normRes)
}