Function reference • rmzqc

All functions
`check_type()`	Checks the value's class type, which should match at least of the types given in any_expected_class_types.
`CV_`	CV_
`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 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
`localFileToURI()`	Convert a local filename, e.g. "./myData/test.mzML" to a proper URI (e.g. "file:///user/bielow/myData/test.mzML")
`MzQCanalysisSoftware-class` `MzQCanalysisSoftware`	Details of the software used to create the QC metrics
`MzQCbaseQuality-class` `MzQCbaseQuality`	Base class of runQuality/setQuality
`MzQCcontrolledVocabulary-class` `MzQCcontrolledVocabulary`	A controlled vocabulary document, usually pointing to an .obo file
`MzQCcvParameter-class` `MzQCcvParameter`	A controlled vocabulary parameter, as detailed in the OBO file
`MzQCDateTime-class` `MzQCDateTime`	An mzQC-formatted date+time in ISO8601 format, as required by the mzQC spec doc.
`MzQCinputFile-class` `MzQCinputFile`	An inputfile within metadata for a run/setQuality
`MzQCmetadata-class` `MzQCmetadata`	The metadata for a run/setQuality
`MzQCmzQC-class` `MzQCmzQC`	Root element of an mzQC document
`MzQCqualityMetric-class` `MzQCqualityMetric`	The central class to store QC information
`MzQCrunQuality-class` `MzQCrunQuality`	A runQuality object. Use to report metrics for individual runs which are independent of other runs.
`MzQCsetQuality-class` `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_charNA()`	Converts a NULL to NA_character_; or returns the argument unchanged otherwise
`NULL_to_NA()`	Converts a NULL to NA; or returns the argument unchanged otherwise
`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.
`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
`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.

Reference

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