CV_                     Define a Singleton class which can hold a CV
                        dictionary (so we do not have to load the .obo
                        files over and over again)
MzQCDateTime-class      An mzQC-formatted date+time in ISO8601 format,
                        as required by the mzQC spec doc.
MzQCanalysisSoftware-class
                        Details of the software used to create the QC
                        metrics
MzQCbaseQuality-class   Base class of runQuality/setQuality
MzQCcontrolledVocabulary-class
                        A controlled vocabulary document, usually
                        pointing to an .obo file
MzQCcvParameter-class   A controlled vocabulary parameter, as detailed
                        in the OBO file
MzQCinputFile-class     An inputfile within metadata for a
                        run/setQuality
MzQCmetadata-class      The metadata for a run/setQuality
MzQCmzQC-class          Root element of an mzQC document
MzQCqualityMetric-class
                        The central class to store QC information
MzQCrunQuality-class    A runQuality object. Use to report metrics for
                        individual runs which are independent of other
                        runs.
MzQCsetQuality-class    A setQuality object. Use it for metrics which
                        are specific to sets, i.e. only for values
                        which only make sense in the set context and
                        cannot be stored as runQuality (see mzQC spec
                        doc).
NULL_to_NA              Converts a NULL to NA; or returns the argument
                        unchanged otherwise
NULL_to_charNA          Converts a NULL to NA_character_; or returns
                        the argument unchanged otherwise
check_type              Checks the value's class type, which should
                        match at least of the types given in
                        any_expected_class_types.
filenameToCV            For a given filename (e.g. "test.mzML"), check
                        the suffix and translate it to an PSI-MS CV
                        term, e.g. 'MS:1000584'
fromDatatoMzQC          Allow conversion of plain named lists of R
                        objects (from jSON) to mzQC objects
fromDatatoMzQCobj       Allow conversion of a plain R object (obtained
                        from jSON) to an mzQC object
getCVDictionary         Parse the content of 'psi-ms.obo', 'pato.obo',
                        and 'uo.obo' from the 'rmzqc/cv/' folder as
                        ontology and return their union
getCVSingleton          Returns the CV singleton. See CV_.
getCVTemplate           Fills a MzQCcvParameter object with
                        id(accession) and name. The value (if any)
                        needs to be set afterwards.
getDefaultCV            Returns an MzQCcontrolledVocabulary which
                        points to the PSI-MS CV which is currently
                        shipped with this package
getDefaultCVVersion     Obtains the current 'data-version' from the
                        MS-CV shipped with this package
getQualityMetricTemplate
                        Fills a MzQCqualityMetric object with
                        id(accession) and name. The value (if any) and
                        unit (if any) need to be set afterwards.
getSyntaxValidator      Get a syntax validator for mzQC
hasFileSuffix           Checks if filepath ends in suffix (ignoring
                        lower/upper case differences). If suffix does
                        not start with a '.' it is prepended
                        automatically.
isUndefined             Tell if a string is undefined (NA or NULL); If
                        yes, and its required by the mzQC standard, we
                        can raise an error.
isValidMzQC             Checks validity (= completeness) of mzQC
                        objects - or lists (JSON arrays) thereof
parseOBO                Get the information of each CV term from an obo
                        file.
readMZQC                Read a JSON file in mzQC format into an
                        MzQCmzQC root object
removeFileSuffix        Removes the last suffix (including the last
                        dot) from a filename. If no dot exists, the
                        full string is returned.
rmzqc                   rmzqc: A package for reading, validating, and
                        writing mzQC files.
toAnalysisSoftware      From an ID, e.g. "MS:1003162" (for PTX-QC), and
                        some additional information, create an
                        'analysisSoftware' node for mzQC
toQCMetric              Create an 'MzQCqualityMetric' object from two
                        inputs
validateFromFile        Syntactically validates an mzQC document which
                        is present as a file.
validateFromObj         Syntactically validates an mzQC document which
                        is already in memory as mzQC root object, as
                        obtained by, e.g. readMZQC().
validateFromString      Syntactically validates an mzQC document which
                        is already in memory as JSON string. e.g. the
                        string " mzQC : "
writeMZQC               Writes a full mzQC object to disk.
