helper_fn.R

# Functions to get omicsData attributes ----------------------------------------

#' Fetch the data_info attribute
#'
#' Retrieves the values in the data_info attribute from an omicsData object.
#'
#' @param omicsData An object of class pepData, proData, metabData, lipidData,
#'                  or nmrData.
#'
#' @return A list containing seven elements:
#'         \itemize{
#'
#'           \item data_scale -- A Character string indicating the scale of the
#'           data in \code{e_data}.
#'
#'           \item norm_info -- A list containing a single element indicating
#'           whether the data in \code{e_data} have been normalized.
#'
#'           \item num_edata -- The number of unique entries present in the
#'           \code{edata_cname} column in \code{e_data}.
#'
#'           \item num_miss_obs -- An integer. The number of missing
#'           observations in \code{e_data}.
#'
#'           \item num_zero_obs -- An integer. The number of zeros
#'           in \code{e_data} for seqData objects.
#'
#'           \item prop_missing -- A number between 0 and 1. The proportion of
#'           missing observations in \code{e_data}.
#'
#'           \item num_samps -- An integer indicating the number of samples or
#'           columns (excluding the identifier column \code{edata_cname}) in
#'           \code{e_data}.
#'
#'           \item data_types -- A character string describing the type of data
#'           in \code{e_data}.
#'
#'         }
#'
#' @export
#' @name get_data_info
#'
get_data_info <- function(omicsData) {
  # Check class of omicsData.
  if (!inherits(omicsData, c(
    "pepData",
    "proData",
    "metabData",
    "lipidData",
    "nmrData",
    "seqData"
  ))) {
    # Lay down an error in the console.
    stop(paste("omicsData must be of class 'pepData', 'proData',",
      "'metabData', 'lipidData', 'nmrData', or 'seqData'",
      sep = " "
    ))
  }

  # Extract and return the data_info attribute.
  return(attr(omicsData, 'data_info'))
}

#' Fetch the normalization status of the data
#'
#' This function returns the norm_info element of the data_info attribute
#' indicating whether the data have been normalized.
#'
#' @param omicsObject an object of the class 'pepData', 'proData', 'metabData',
#'   'lipidData', 'nmrData', 'statRes', or 'trelliData', usually created by
#'   \code{\link{as.pepData}}, \code{\link{as.proData}},
#'   \code{\link{as.metabData}}, \code{\link{as.lipidData}},
#'   \code{\link{as.nmrData}}, \code{\link{imd_anova}}, or
#'   \code{\link{as.trelliData}} respectively.
#'
#' @return A logical value indicating whether the data have been normalized.
#'
#' @export
#' @name get_data_norm
#'
get_data_norm <- function(omicsObject) {
  # check that omicsObject is of appropriate class #
  if (!inherits(omicsObject, c(
    "pepData", "proData", "metabData", "lipidData",
    "nmrData", "statRes", "trelliData", "seqData"
  )))
    stop(paste("omicsData must be of class 'pepData', 'proData', 'metabData',",
      "'lipidData', 'nmrData', 'seqData', 'statRes', or 'trelliData'",
      sep = " "
    ))

  return(attr(omicsObject, "data_info")$norm_info$is_normalized)
}

#' Fetch the meta_info attribute
#'
#' Retrieves the values in the meta_info attribute from an omicsData object.
#'
#' @param omicsData An object of class pepData, proData, metabData, lipidData,
#'                  or nmrData.
#'
#' @return A list containing two elements:
#'         \itemize{
#'
#'           \item meta_data -- Logical. Indicates if the \code{e_meta} data
#'           frame was provided.
#'
#'           \item num_emeta -- The number of unique entries present in the
#'           \code{emeta_cname} column in \code{e_meta}.
#'
#'         }
#'
#' @export
#' @name get_meta_info
#'
get_meta_info <- function(omicsData) {
  # Check class of omicsData.
  if (!inherits(omicsData, c(
    "pepData",
    "proData",
    "metabData",
    "lipidData",
    "nmrData",
    "seqData"
  ))) {
    # Lay down an error in the console.
    stop(paste("omicsData must be of class 'pepData', 'proData',",
      "'metabData', 'lipidData', 'nmrData', or 'seqData'",
      sep = " "
    ))
  }

  # Extract and return the meta_info attribute.
  return(attr(omicsData, 'meta_info'))
}

#' Fetch the filters attribute
#'
#' Retrieves the values in the filters attribute from an omicsData object.
#'
#' @param omicsData An object of class pepData, proData, metabData, lipidData,
#'                  or nmrData.
#'
#' @return A list containing filter class objects. Each element in this list
#'         corresponds to a filter applied to the data. The filters will be
#'         listed in the order they were applied. A filter object contains two
#'         elements:
#'         \itemize{
#'
#'           \item threshold -- The threshold used to filter \code{e_data}. This
#'           value depends on the type of filter applied.
#'
#'           \item filtered -- A vector containing the identifiers from the
#'           \code{edata_cname} column that will be filtered.
#'
#'           \item method -- A character string indicating the type of method
#'           used to filter. This only applies when imdanova_filter is used.
#'
#'         }
#'
#' @export
#' @name get_filters
#'
get_filters <- function(omicsData) {
  # Check class of omicsData.
  if (!inherits(omicsData, c(
    "pepData",
    "proData",
    "metabData",
    "lipidData",
    "nmrData",
    "seqData"
  ))) {
    # Lay down an error in the console.
    stop(paste("omicsData must be of class 'pepData', 'proData',",
      "'metabData', 'lipidData', 'nmrData', or 'seqData'",
      sep = " "
    ))
  }

  # Send a message if the filters object is empty.
  if (length(attr(omicsData, 'filters')) == 0) {
    message("No filters have been applied.")

    # Return NULL if there are no filters for the pmart app people.
    return(NULL)
  } else {
    # Extract and return the filters attribute.
    return(attr(omicsData, 'filters'))
  }
}

#' Extracts the types of filters that have been applied. This function will be
#' used at the beginning of the applyFilt function to give a warning if the
#' same type of filter has already been applied.
#'
#' Retrieves the values in the filters attribute from an omicsData object.
#'
#' @param omicsData An object of class pepData, proData, metabData, lipidData,
#'                  seqData, or nmrData.
#'
#' @return vector of filters used on omicsData
#'
get_filter_type <- function(omicsData) {
  # Store the filters attribute from the previous filters (if any).
  pFilters <- suppressMessages(get_filters(omicsData))
  # pFilters <- attr(omicsData, 'filters')

  # Determine the length of the filters attribute. The length corresponds to the
  # number of filters applied previously.
  nFilters <- length(pFilters)

  # Check the length of filters.
  if (nFilters == 0) {
    # If no filters have been applied return NULL.
    return(NULL)
  } else {
    # Fabricate a vector to hold the filter types.
    pTypes <- vector(length = nFilters)

    # Loop through each filter.
    for (e in 1:nFilters) {
      # Extract the filter type.
      pTypes[[e]] <- pFilters[[e]]$type
    }

    # Return the character vector containing the filter types!!
    return(pTypes)
  }
}

#' \bold{DEPRECATED}: Fetch the check.names attribute
#'
#' \emph{Retrieves the value in check.names attribute from an omicsData object.}
#' \bold{This function has been deprecated in favor of handling checking names
#' externally, and will always return FALSE.}
#'
#' @param omicsData An object of class pepData, proData, metabData, lipidData,
#'                  or nmrData.
#'
#' @return A logical value indicating if the syntax of the column names in a
#'         data frame should be checked. See \code{\link[base]{data.frame}} for
#'         more details.
#'
#' @export
#' @name get_check_names
#'
get_check_names <- function(omicsData) {
  warning("get_check_names: function is deprecated")

  # Check class of omicsData.
  if (!inherits(omicsData, c(
    "pepData",
    "proData",
    "metabData",
    "lipidData",
    "nmrData",
    "seqData"
  ))) {
    # Lay down an error in the console.
    stop(paste("omicsData must be of class 'pepData', 'proData',",
      "'metabData', 'lipidData', 'nmrData', or 'seqData'",
      sep = " "
    ))
  }

  return(FALSE)
}

#' Fetch the isobaric_info attribute
#'
#' Retrieves the values in the isobaric_info attribute from an omicsData object.
#'
#' @param omicsData An object of class pepData, proData, metabData, lipidData,
#'                  or nmrData.
#'
#' @return A list containing the following six elements:
#'         \itemize{
#'
#'           \item exp_cname --
#'
#'           \item channel_cname --
#'
#'           \item refpool_channel --
#'
#'           \item refpool_cname --
#'
#'           \item refpool_notation --
#'
#'           \item norm_info -- A list containing a single logical element that
#'           indicates whether the data have been normalized to a reference
#'           pool.
#'
#'         }
#'
#' @export
#' @name get_isobaric_info
#'
get_isobaric_info <- function(omicsData) {
  # Check class of omicsData.
  if (!inherits(omicsData, c(
    "isobaricpepData",
    "pepData"
  ))) {
    # Lay down an error in the console.
    stop(paste("omicsData must be of class 'isobaricpepData' and 'pepData'",
      sep = " "
    ))
  }

  # Extract and return the isobaric_info attribute.
  return(attr(omicsData, 'isobaric_info'))
}

#' Fetch the isobaric normalization info
#'
#' This function returns the norm_info element of the isobaric_info attribute
#' which indicates if the data have been isobaric normalized.
#'
#' @param omicsData an object of the class 'pepData', 'isobaricpepData' or
#'   'proData', usually created by \code{\link{as.pepData}},
#'   \code{\link{as.isobaricpepData}}.
#'
#' @return A logical value indicating whether the data have been isobaric
#'   normalized.
#'
#' @export
#' @name get_isobaric_norm
#'
get_isobaric_norm <- function(omicsData) {
  # check that omicsData is of appropriate class #
  if (!inherits(omicsData, c("pepData", "proData", "isobaricpepData")))
    stop("omicsData must be of class 'pepData', 'proData' or 'isobaricpepData'")

  return(attr(omicsData, "isobaric_info")$norm_info$is_normalized)
}

#' Fetch the nmr_info attribute
#'
#' Retrieves the values in the nmr_info attribute from an omicsData object.
#'
#' @param omicsData An object of class pepData, proData, metabData, lipidData,
#'                  or nmrData.
#'
#' @return A list containing the following three elements:
#'         \itemize{
#'
#'           \item metabolite_name --
#'
#'           \item sample_property_cname --
#'
#'           \item norm_info -- A list containing two logical elements that
#'           indicate i) whether the data have been normalized to a spiked in
#'           metabolite or to a property taking sample-specific values and ii)
#'           whether the data have been back transformed so the values are on a
#'           similar scale to the raw values before normalization.
#'
#'         }
#'
#' @export
#' @name get_nmr_info
#'
get_nmr_info <- function(omicsData) {
  ############################## should we add "nmrnormRes" objects? ###########
  #### should this be restricted to nmr class?  
  #### should we open up other calls to all classes? ########

  # Check class of omicsData.
  if (!inherits(omicsData, c(
    "pepData",
    "proData",
    "metabData",
    "lipidData",
    "nmrData"
  ))) {
    # Lay down an error in the console.
    stop(paste("omicsData must be of class 'pepData', 'proData',",
      "'metabData', 'lipidData', or 'nmrData'",
      sep = " "
    ))
  }

  # Extract and return the nmr_info attribute.
  return(attr(omicsData, 'nmr_info'))
}

#' Fetch the NMR normalization info
#'
#' This function returns the norm_info element of the nmr_info attribute which
#' indicates if the data have been NMR normalized.
#'
#' @param omicsData an object of the class 'nmrData'.
#'
#' @return A logical value indicating whether the data have been NMR normalized.
#'
#'
#' @export
#' @name get_nmr_norm
#'
get_nmr_norm <- function(omicsData) {
  # check that omicsData is of appropriate class #
  if (!inherits(omicsData, "nmrData"))
    stop("omicsData must be of class 'nmrData'")

  return(attr(omicsData, "nmr_info")$norm_info$is_normalized)
}

#' Fetch the group_DF attribute
#'
#' Retrieves the values in the group_DF attribute from an omicsData object.
#'
#' @param omicsData An object of class pepData, proData, metabData, lipidData,
#'                  or nmrData.
#'
#' @return A data.frame with columns for sample ID and group. If two main
#'         effects are provided the original main effect levels for each sample
#'         are returned as the third and fourth columns of the data frame.
#'         Additionally, the covariates provided will be listed as attributes of
#'         this data frame.
#'
#' @export
#' @name get_group_DF
#'
get_group_DF <- function(omicsData) {
  # Check class of omicsData.
  if (!inherits(omicsData, c(
    "pepData",
    "proData",
    "metabData",
    "lipidData",
    "nmrData",
    "seqData"
  ))) {
    # Lay down an error in the console.
    stop(paste("omicsData must be of class 'pepData', 'proData',",
      "'metabData', 'lipidData', 'nmrData', or 'seqData'",
      sep = " "
    ))
  }

  # Extract and return the group_DF attribute.
  return(attr(omicsData, 'group_DF'))
}

#' Fetch the original data scale
#'
#' Retrieves the character string indicating the scale the data was originally
#' on when read into R.
#'
#' @param omicsObject an object of class 'pepData', 'proData', 'metabData',
#'  'lipidData', or 'nmrData'.
#'
#' @return A character string.
#'
#' @export
#' @name get_data_scale_orig
#'
get_data_scale_orig <- function(omicsObject) {
  # Check that the input is an appropriate class.
  if (!inherits(omicsObject, c(
    "pepData", "proData", "metabData",
    "lipidData", "nmrData", 'seqData'
  ))) {
    # Halt! You are using an unholy input object. Come back when your data is
    # decent.
    stop("omicsObject is not an accepted class.")
  }

  return(attr(omicsObject, "data_info")$data_scale_orig)
}

#' Fetch the current data scale
#'
#' This function returns current data scale which may be different from the
#' original data scale (if \code{edata_transform} was used).
#'
#' @param omicsObject an object of the class 'pepData', 'proData', 'metabData',
#'   'lipidData', 'nmrData', 'statRes', or 'trelliData', usually created by
#'   \code{\link{as.pepData}}, \code{\link{as.proData}},
#'   \code{\link{as.metabData}}, \code{\link{as.lipidData}},
#'   \code{\link{as.nmrData}}, \code{\link{imd_anova}}, or
#'   \code{\link{as.trelliData}} respectively.
#'
#' @return a character string describing data scale
#'
#' @export
#' @name get_data_scale
#'
get_data_scale <- function(omicsObject) {
  # check that omicsObject is of appropriate class #
  if (!inherits(omicsObject, c(
    "pepData", "proData", "metabData", "lipidData",
    "nmrData", "statRes", "trelliData", 'seqData'
  )))

    stop(paste("omicsData must be of class 'pepData', 'proData', 'metabData',",
      "'lipidData', 'nmrData', 'seqData', 'statRes', or 'trelliData'",
      sep = " "
    ))

  return(attr(omicsObject, "data_info")$data_scale)
}

#' Fetch the e_data column name
#'
#' This function returns the name of the column in e_data that contains the
#' biomolecule IDs.
#'
#' @param omicsObject an object of the class 'pepData', 'proData', 'metabData',
#'   'lipidData', 'nmrData', 'statRes', or 'trelliData', usually created by
#'   \code{\link{as.pepData}}, \code{\link{as.proData}},
#'   \code{\link{as.metabData}}, \code{\link{as.lipidData}},
#'   \code{\link{as.nmrData}}, \code{\link{imd_anova}}, or
#'   \code{\link{as.trelliData}} respectively.
#'
#' @return a character string describing e_data cname
#'
#' @export
#' @name get_edata_cname
#'
get_edata_cname <- function(omicsObject) {
  # check that omicsObject is of appropriate class #
  if (!inherits(omicsObject, c(
    "pepData", "proData", "metabData", "lipidData",
    "nmrData", 'seqData', "statRes", "trelliData"
  )))
    stop(paste("omicsData must be of class 'pepData', 'proData', 'metabData',",
      "'lipidData', 'nmrData', 'seqData', 'statRes', or 'trelliData'",
      sep = " "
    ))

  return(attr(omicsObject, "cnames")$edata_cname)
}

#' Fetch the f_data column name
#'
#' This function returns the name of the column in f_data that contains the
#' names of the samples.
#'
#' @param omicsObject an object of the class 'pepData', 'proData', 'metabData',
#'   'lipidData', 'nmrData', 'statRes', or 'trelliData', usually created by
#'   \code{\link{as.pepData}}, \code{\link{as.proData}},
#'   \code{\link{as.metabData}}, \code{\link{as.lipidData}},
#'   \code{\link{as.nmrData}}, \code{\link{imd_anova}}, or
#'   \code{\link{as.trelliData}} respectively.
#'
#' @return a character string describing f_data cname
#'
#' @export
#' @name get_fdata_cname
#'
get_fdata_cname <- function(omicsObject) {
  # check that omicsObject is of appropriate class #
  if (!inherits(omicsObject, c(
    "pepData", "proData", "metabData", "lipidData",
    "nmrData", 'seqData', "statRes", "trelliData"
  )))
    stop(paste("omicsData must be of class 'pepData', 'proData', 'metabData',",
      "'lipidData', 'nmrData', 'seqData', 'statRes', or 'trelliData'",
      sep = " "
    ))

  return(attr(omicsObject, "cnames")$fdata_cname)
}

#' Fetch the e_meta column name
#'
#' This function returns the name of the column in e_meta that contains the
#' mapping variable IDs.
#'
#' @param omicsObject an object of the class 'pepData', 'proData', 'metabData',
#'   'lipidData', 'nmrData', 'statRes', or 'trelliData', usually created by
#'   \code{\link{as.pepData}}, \code{\link{as.proData}},
#'   \code{\link{as.metabData}}, \code{\link{as.lipidData}},
#'   \code{\link{as.nmrData}}, \code{\link{imd_anova}}, or
#'   \code{\link{as.trelliData}} respectively.
#'
#' @return a character string describing e_meta cname
#'
#' @export
#' @name get_emeta_cname
#'
get_emeta_cname <- function(omicsObject) {
  # check that omicsObject is of appropriate class #
  if (!inherits(omicsObject, c(
    "pepData", "proData", "metabData", "lipidData",
    "nmrData", 'seqData', "statRes", "trelliData"
  )))
    stop(paste("omicsData must be of class 'pepData', 'proData', 'metabData',",
      "'lipidData', 'nmrData', 'seqData', 'statRes', or 'trelliData'",
      sep = " "
    ))

  if (is.null(omicsObject$e_meta) && inherits(omicsObject, "statRes"))
    stop(paste("emeta_cname of input statsRes object is dependent on",
      "omicsData used in imd_anova; emeta_cname is NULL",
      sep = " "
    ))

  return(attr(omicsObject, "cnames")$emeta_cname)
}

#' Functions to set omicsData attributes ----------------------------------------
#'
#' Create a set function that will return the value for each attribute. For
#' example, set_data_info will perform all of the calculations to fill in the
#' data_info attribute. These functions will be called in the as.xxx functions
#' to create an xxxData object but can be used individually to update any one of
#' the attributes at a later time.

#' Sets/updates the values in the data_info attribute
#'
#' @param e_data,edata_cname,data_scale_orig,data_scale,data_types,norm_info,is_normalized,batch_info,is_bc 
#'  See the \code{as.omicsData} functions, e.g. \code{\link{as.lipidData}}
#'
#' @return A list of edited data_info to replace the attribute in the
#'  omicsData object.
#'
#' @keywords internal 
set_data_info <- function(e_data,
                          edata_cname,
                          data_scale_orig,
                          data_scale,
                          data_types,
                          norm_info,
                          is_normalized,
                          batch_info,
                          is_bc) {
  # Identify the column number that contains the IDs.
  id_col <- which(names(e_data) == edata_cname)

  # Count the number of missing values in e_data.
  if (data_scale == "counts") {
    num_zero_obs <- sum(e_data[, -id_col] == 0)

    # Calculate the proportion of missing data in e_data.
    prop_zeros <- mean(e_data[, -id_col] == 0)
  } else {
    num_miss_obs <- sum(is.na(e_data[, -id_col]))

    # Calculate the proportion of missing data in e_data.
    prop_missing <- mean(is.na(e_data[, -id_col]))
  }

  # Extract the number of things (e.g., peptides, lipids, metabolites, ...).
  num_edata <- nrow(e_data)

  # Procure the number of samples.
  num_samps <- ncol(e_data) - 1

  # Set data normalization information.
  norm_info$is_normalized <- is_normalized

  batch_info$is_bc <- is_bc

  # Return all of the information that belongs in the data_info attribute.

  if (data_scale == "counts") {
    return(list(
      data_scale_orig = data_scale_orig,
      data_scale = data_scale,
      norm_info = norm_info,
      num_edata = num_edata,
      num_zero_obs = num_zero_obs,
      prop_zeros = prop_zeros,
      num_samps = num_samps,
      data_types = data_types,
      batch_info = batch_info
    ))
  } else {
    return(list(
      data_scale_orig = data_scale_orig,
      data_scale = data_scale,
      norm_info = norm_info,
      num_edata = num_edata,
      num_miss_obs = num_miss_obs,
      prop_missing = prop_missing,
      num_samps = num_samps,
      data_types = data_types,
      batch_info = batch_info
    ))
  }
}

#' Sets/updates the values in the meta_info attribute
#'
#' @param e_meta,emeta_cname See the \code{as.omicsData} functions, e.g. 
#'  \code{\link{as.lipidData}} 
#'
#' @return A list containing all the elements in the meta_info attribute:
#'        (list all attributes)
#' 
#' @keywords internal
#'
set_meta_info <- function(e_meta,
                          emeta_cname) {
  # Determine if meta data is present.
  meta_data <- ifelse(is.null(e_meta), FALSE, TRUE)

  # Test if emeta_cname is not null.
  if (!is.null(emeta_cname)) {
    # Enumerate the number of unique proteins that map to a peptide in e_data.
    # When using other data (e.g., lipid or metabolite) this counts the number
    # of unique mapping variables associated with a biomolecule.
    num_emeta <- length(unique(e_meta[, emeta_cname]))
  } else {
    # If emeta_cname is null set the number of proteins to null.
    num_emeta <- NULL
  }

  # Return the list of meta attributes.
  return(list(
    meta_data = meta_data,
    num_emeta = num_emeta
  ))
}

#' Sets/updates the values in the isobaric_info attribute.
#'
#' @param exp_cname,channel_cname,refpool_channel,refpool_cname,refpool_notation,norm_info,isobaric_norm See \code{\link{normalize_isobaric}}
#'
#' @return A list containing all the elements in the isobaric_info attribute:
#'         (list all attributes)
#'
#' @keywords internal
set_isobaric_info <- function(exp_cname,
                              channel_cname,
                              refpool_channel,
                              refpool_cname,
                              refpool_notation,
                              norm_info,
                              isobaric_norm) {
  # Set the elements of the norm_info list.
  norm_info$is_normalized <- isobaric_norm

  # Return the list of isobaric_info attributes.
  return(list(
    exp_cname = exp_cname,
    channel_cname = channel_cname,
    refpool_channel = refpool_channel,
    refpool_cname = refpool_cname,
    refpool_notation = refpool_notation,
    norm_info = norm_info
  ))
}

#'  Sets/updates the values in the nmr_info attribute.
#'
#' @param metabolite_name
#'
#' @param sample_property_cname
#'
#' @param norm_info
#'
#' @param nmr_norm
#'
#' @param backtransform
#'
#' @return A list containing all the elements in the nmr_info attribute:
#'         (list all attributes)
#' 
#' @keywords internal
#'
set_nmr_info <- function(metabolite_name,
                         sample_property_cname,
                         norm_info,
                         nmr_norm,
                         backtransform) {
  # Set the elements of the norm_info list.
  norm_info$is_normalized <- nmr_norm
  norm_info$backtransform <- backtransform

  # Return the list of objects belonging to this attribute.
  return(list(
    metabolite_name = metabolite_name,
    sample_property_cname = sample_property_cname,
    norm_info = norm_info
  ))
}

#' Sets/updates the filters attribute with a filter class object.
#'
#' This function will create a filter class object. The output will always have
#' the same elements but not all of them will be used for every filter type. This
#' object will be appended to the list in the filters attribute for an omicsData
#' object.
#'
#' @param type The type of filter, see \code{filter_objects.R}
#'
#' @param threshold The threshold for filtering applied, if applicable.
#'
#' @param filtered The samples/biomolecules that are filtered.
#'
#' @param method A list of metadata about what method was used in applying the 
#'  filter.
#'
#' @return A list containing all the elements in the filters attribute:
#'         (list all attributes)
#' 
#' @keywords internal
set_filter <- function(type,
                       threshold,
                       filtered,
                       method) {
  # Create an object that will have the filter elements and class added to it
  # later (in the next 10 lines or so).
  filta <- list()

  # Add the class of the filter being applied to filta.
  filta$type <- type

  # Add threshold to filta.
  filta$threshold <- threshold

  # Append filtered to the filta list.
  filta$filtered <- filtered

  # Affix the filter method to filta. This is only used with imdanovaFilt.
  filta$method <- method

  # Create the filter class.
  class(filta) = "filter"

  return(filta)
}

#' \bold{DEPRECATED}: Set check.names attribute of omicsData object
#'
#' \emph{This function sets the check.names attribute of an omicsData object.}
#' \bold{This function has been deprecated in favor of handling checking names
#' externally and will return an unmodified omicsData.}
#'
#' @param omicsData an object of the class 'pepData', 'proData', 'metabData',
#'   'lipidData', or 'nmrData', usually created by \code{\link{as.pepData}},
#'   \code{\link{as.proData}}, \code{\link{as.metabData}},
#'   \code{\link{as.lipidData}}, or \code{\link{as.nmrData}}, respectively.
#' @param set_to logical indicating what to set check.names attribute to.
#'   Defaults to TRUE.
#'
#' @return omicsData object with updated check.names attribute
#'
#' @export
#' @name set_check_names
#'
set_check_names <- function(omicsData, set_to = TRUE) {
  warning("set_check_names: function is deprecated")

  # check that omicsData is of appropriate class #
  if (!inherits(omicsData, c(
    "pepData", "proData", "metabData",
    "lipidData", "nmrData", "seqData"
  )))
    stop(paste("omicsData must be of class 'pepData', 'proData',",
      "'metabData', 'lipidData', 'nmrData', or 'seqData'",
      sep = " "
    ))

  return(omicsData)
}

# Functions to get statRes attributes ------------------------------------------

#' Return comparisons of statRes object
#'
#' This function returns comparisons from statRes or trelliData object
#'
#' @param compObj is an object with the comparison attribute; specifically
#'   objects of class 'statRes' and 'trelliData' objects derived from 'statRes'
#'   objects in \code{\link{as.trelliData}}
#' @return returns a data frame with comparisons and their indices
#' @examplesIf requireNamespace("pmartRdata", quietly = TRUE)
#' library(pmartRdata)
#'
#' my_prodata = group_designation(
#'   omicsData = pro_object,
#'   main_effects = c("Phenotype")
#' )
#'
#' imdanova_Filt = imdanova_filter(omicsData = my_prodata)
#'
#' my_prodata = applyFilt(
#'   filter_object = imdanova_Filt,
#'   omicsData = my_prodata,
#'   min_nonmiss_anova = 2
#' )
#'
#' imd_anova_res = imd_anova(
#'   omicsData = my_prodata,
#'   test_method = 'comb',
#'   pval_adjust_a_multcomp = 'bon',
#'   pval_adjust_g_multcomp = 'bon'
#' )
#'
#' result = get_comparisons(imd_anova_res)
#'
#' @export
#' @name get_comparisons
#'
get_comparisons <- function(compObj) {
  # check that compObj object is of 'statRes' or 'trelliData' class
  if (!inherits(compObj, c("statRes", "trelliData")))
    stop("object must be of class 'statRes' or 'trelliData'")

  # check that compObj object is of 'statRes' or 'trelliData' class
  if (inherits(compObj, "trelliData") && 
      is.null(attr(compObj, "comparisons"))) {
    return(NULL)
  } else {
    # pull comparisons attribute
    comp = attr(compObj, "comparisons")

    result = data.frame(
      "comparisons" = as.character(comp),
      "index" = 1:length(comp),
      stringsAsFactors = FALSE
    )

    return(result)
  }
}

#' Return data_class of statRes or trelliData object
#'
#' This function returns data_class attribute from statRes or trelliData object,
#' inherited from the omicsData used in \code{\link{imd_anova}} or
#' \code{\link{as.trelliData}}
#'
#' @param dcObj an object of class 'statRes' or 'trelliData'
#'
#' @return returns the data_class attribute from a 'statRes' or 'trelliData'
#'   object
#'
#' @examplesIf requireNamespace("pmartRdata", quietly = TRUE)
#' library(pmartRdata)
#'
#' my_prodata = group_designation(
#'   omicsData = pro_object,
#'   main_effects = c("Phenotype")
#' )
#'
#' imdanova_Filt = imdanova_filter(omicsData = my_prodata)
#'
#' my_prodata = applyFilt(
#'   filter_object = imdanova_Filt,
#'   omicsData = my_prodata,
#'   min_nonmiss_anova = 2
#' )
#'
#' imd_anova_res = imd_anova(
#'   omicsData = my_prodata,
#'   test_method = 'comb',
#'   pval_adjust_a_multcomp = 'bon',
#'   pval_adjust_g_multcomp = 'bon'
#' )
#'
#' result = get_data_class(imd_anova_res)
#'
#' @export
#' @name get_data_class
#'
get_data_class <- function(dcObj) {
  # check that compObj object is of 'statRes' class
  if (!inherits(dcObj, c("statRes", "trelliData")))
    stop("dcObj object must be of class 'statRes' or 'trelliData'")

  return(attr(dcObj, "data_class"))
}

#' Get group table
#'
#' This function returns a table with number of samples per group
#'
#' @param omicsObject an object of the class 'pepData', 'proData', 'metabData',
#'   'lipidData', 'nmrData', 'statRes', or 'trelliData', usually created by
#'   \code{\link{as.pepData}}, \code{\link{as.proData}},
#'   \code{\link{as.metabData}}, \code{\link{as.lipidData}},
#'   \code{\link{as.nmrData}}, \code{\link{imd_anova}}, or
#'   \code{\link{as.trelliData}} respectively.
#'
#' @return a table containing number of samples per group
#'
#' @export
#' @name get_group_table
#'
get_group_table <- function(omicsObject) {
  # check that omicsObject is of appropriate class #
  if (!inherits(omicsObject, c(
    "pepData", "proData", "metabData", "lipidData",
    "nmrData", "seqData", "statRes", "trelliData"
  )))
    stop(paste("omicsData must be of class 'pepData', 'proData', 'metabData',",
      "'lipidData', 'nmrData', 'seqData', 'statRes', or 'trelliData'",
      sep = " "
    ))

  if (is.null(attr(omicsObject, "group_DF"))) {
    return(NULL)
  } else {
    # should the result be constructed from omicsObject$f_data or from the
    # group_DF attr? if so...
    group = attr(omicsObject, "group_DF")$Group

    return(table(group))
  }
}

#' Helper to find the names of columns of a data.frame that contain exactly all
#' the elements of an input column
#'
#' @param df A data.frame whose columns we want to match to some query column.
#' @param col Vector of values which will be compared to a column in df.
#'
#' @return vector of column names of df that contain exactly all the elements of
#' the input column
#'
#' @keywords internal
column_matches_exact <- function(df, col) {
  diffs = lapply(df, function(df_col) {
    length(setdiff(
      union(df_col, col),
      intersect(df_col, col)
    ))
  })

  matched_cnames = names(diffs)[which(diffs == 0)]

  return(matched_cnames)
}

#' Custom message function to pretty-print text with newlines so you can follow
#' character limit guidelines in source code.
#' @noRd
wrap_message <- function(..., prefix = " ", initial = "") {
  message(strwrap(..., prefix = prefix, initial = initial))
}