R/combinerCheck.R

In hhabra/Combiner: Method for Combining LC-MS Metabolomics Feature Measurements

#' @title Obtain Errors for metabCombiner Object Checks
#'
#' @description This function stores and returns a customized error message
#' when checking the validity of certain objects.
#'
#' @param errNo integer error code.
#'
#' @param type  character object type (either "combinedTable", "metabCombiner"
#' or "metabData")
#'
#' @param error character. If "stop", gives an error message; if "warning",
#' provides a warning message; if "silent", returns silently
#'
#' @details In certain functions, an object must be checked for correctness. A
#' \code{metabData} must have a properly formatted dataset with the correct
#' column names & types.A \code{metabCombiner} must have properly formatted
#' \code{combinedTable}, with expected names and columns. If one of these
#' conditions is not met, a non-zero numeric code is returned and this function
#' is used to print a specific error message corresponding to the appropriate
#' object and error code.
#'
#' @return A customized error message for specific object check.
combinerCheck <- function(errNo, type, error = "stop"){
    if(errNo == 0)
        return(invisible())

    errors = switch(type,
        "combinedTable" =
            paste(
            c("combinedTable is not a data frame",
            "combinedTable has fewer than expected columns",
            "combinedTable is empty",
            "combinedTable column names different from expected column names",
            "combinedTable column classes different from expected classes",
            "at least one missing or invalid group number in combinedTable"),
            "; see: help(isCombinedTable)", sep = ""),
        "metabCombiner" =
            c("input object is not of class 'metabCombiner'",
            "combinedTable in input object is invalid",
            "duplicate dataset identifiers not allowed",
            "rowID mismatch between combinedTable and featData"
            ),
        "metabData" =
            c("input object is not of class 'metabData'",
            "empty data in input object",
            "data in input object has fewer than expected columns",
            "data in input object has invalid column names",
            "data in input object has invalid column classes")
        )
    if(error == "stop")
        stop(errors[errNo])
    else if(error == "warning")
        warning(errors[errNo])
    else
        return(invisible())
}



combinerNames <- function(){
    return(c("rowID", "idx","idy","mzx","mzy","rtx","rty","rtProj","Qx","Qy",
      "group","score","rankX","rankY","adductx","adducty"))
}



#' @title Determine \code{combinedTable} Validity
#'
#' @description Checks whether input object is a valid metabData.Returns an
#' integer code if invalid. Function is used alongside \code{combinerCheck}.
#'
#' @details a proper \code{combinedTable} must have these characteristics to
#' be deemed valid for \code{metabCombiner} operations:
#'
#' 1) It must be a data.frame with at least 16 columns and at least 1 row
#'
#' 2) The first 16 columns must be named "rowID", "idx","idy","mzx","mzy","rtx",
#'    "rty", "rtProj","Qx","Qy","group","score","rankX","rankY","adductx", &
#'    "adducty" in this exact order
#'
#' 3) The first 16 columns must be of class: "numeric" "character","character",
#'    "numeric","numeric","numeric", "numeric", "numeric","numeric","numeric",
#'    "integer", "numeric", "integer", "integer","character", "character"
#'
#' 4)  The group column must have no missing or negative values
#'
#' Failing any one of these criteria causes an error
#'
#' @param object  Any R object.
#'
#' @return 0 if object is a valid Combiner Table; an integer code otherwise
isCombinedTable <- function(object){
    if(!is.data.frame(object))
        return(1)

    expected <- combinerNames()

    if(ncol(object) <= length(expected)) return(2)
    if(nrow(object) == 0)  return(3)

    if(!identical(names(object)[seq(1,length(expected))], expected))
        return(4)

    coltypes <- as.character(lapply(object, class))
    correct_types <- c("character","character", "numeric","numeric","numeric",
                        "numeric", "numeric","numeric","numeric","integer",
                        "numeric", "integer", "integer","character","character")

    if(!identical(coltypes[seq(2,length(expected))], correct_types))
        return(5)

    if(any(is.na(object[["group"]])) | any(object[["group"]] < 0))
        return(6)

    return(0)
}


##
#' @title Determine if object is a valid metabCombiner object
#'
#' @description Checks whether input object is a valid metabCombiner.Returns an
#' integer code if invalid. Function is used alongside \code{combinerCheck}.
#'
#' @param object Any R object.
#'
#' @return 0 if object is a valid metabData object; an integer code otherwise
isMetabCombiner <- function(object){
    if(!methods::is(object,"metabCombiner"))
        return(1)

    combined_table_code <- isCombinedTable(combinedTable(object))

    if(combined_table_code){
        combinerCheck(combined_table_code, "combinedTable", "warning")
        return(2)
    }

    if(any(duplicated(datasets(object))))
        return(3)

    if(!identical(combinedTable(object)[["rowID"]],featData(object)[["rowID"]]))
        return(4)

    return(0)
}

#'
#' @title Determine validity of input metabData object
#'
#' @description Checks whether input object is a valid metabData.Returns an
#' integer code if invalid. Function is used alongside \code{combinerCheck}.
#'
#' @param object  Any R object
#'
#' @return 0 if object is a valid metabData object; an integer code otherwise.
##
isMetabData <- function(object){
    if(!methods::is(object, "metabData"))
        return(1)
    data <- getData(object)
    expected <- c("rowID","id", "mz", "rt", "adduct", "Q")
    if(ncol(data) <= length(expected))
        return(2)
    if(nrow(data) == 0)
        return(3)
    if(!identical(names(data)[seq(1,length(expected))], expected))
        return(4)
    coltypes <- as.character(lapply(data, class))
    expected_types <- c("integer","character","numeric","numeric",
                        "character","numeric")
    if(!identical(coltypes[seq(1,length(expected))], expected_types))
        return(5)

    return(0)
}