CV_                     CV_
MzQCDateTime            An mzQC-formatted date+time in ISO8601 format,
                        as required by the mzQC spec doc.
MzQCanalysisSoftware    Details of the software used to create the QC
                        metrics
MzQCbaseQuality         Base class of runQuality/setQuality
MzQCbaseQuality_getMetric
                        Extract a certain metric from a runQuality's
                        list of MzQCqualityMetric
MzQCcontrolledVocabulary
                        A controlled vocabulary document, usually
                        pointing to an .obo file
MzQCcvParameter         A controlled vocabulary parameter, as detailed
                        in the OBO file
MzQCinputFile           An inputfile within metadata for a
                        run/setQuality
MzQCmetadata            The metadata for a run/setQuality
MzQCmzQC                Root element of an mzQC document
MzQCqualityMetric       The central class to store QC information
MzQCrunQuality          A runQuality object. Use to report metrics for
                        individual runs which are independent of other
                        runs.
MzQCsetQuality          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         Fetch and parse the 'psi-ms.obo' and some
                        metadata from the usual sources to use as
                        ontology.
getCVInfo               Returns an 'MzQCcontrolledVocabulary' for the
                        currently used CV (see 'getCVSingleton') using
                        'getCVSingleton()$getData()$URI' and $version.
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 for the
                        currently used CV (see 'getCVSingleton')
getLatest_PSICV_URL     Get the latest PSI-MS CV release URL
getLocal_CV_Version     Obtains the 'data-version' from a local (i.e.
                        non-url) PSI-MS-CV
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 variable's value is undefined (NA or
                        NULL); If yes, and it is required by the mzQC
                        standard, we can raise an error.
isValidMzQC             Checks validity (= completeness) of mzQC
                        objects - or lists (JSON arrays) thereof
localFileToURI          Convert a local filename, e.g.
                        "./myData/test.mzML" to a proper URI (e.g.
                        "file:///user/bielow/myData/test.mzML")
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
readMZQCFromJSON        Read a JSON object 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.
removeIfExists          Remove a file, if it exists (useful for
                        temporary files which may or may not have been
                        created)
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 (id and value).
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.
