| check_field_exists | Check if a field exists in data and warn if it doesn't, then... |
| check_type | Checks the value's class type, which should match at least of... |
| checkUnexpectedFields | Check for unexpected fields in data and warn if any are found |
| CV_ | CV_ |
| filenameToCV | For a given filename (e.g. "test.mzML"), check the suffix and... |
| fromDatatoMzQC | Allow conversion of plain named lists of R objects (from... |
| fromDatatoMzQCobj | Allow conversion of a plain R object (obtained from jSON) to... |
| getCVDictionary | Fetch and parse the 'psi-ms.obo' and some metadata from the... |
| getCVInfo | Returns an 'MzQCcontrolledVocabulary' for the currently used... |
| getCVSingleton | Returns the CV singleton. See 'CV_'. |
| getCVTemplate | Fills a MzQCcvParameter object with id(accession) and name.... |
| getDefaultCV | Returns an MzQCcontrolledVocabulary for the currently used CV... |
| 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)... |
| getOptionalValue | Get an optional value from data, using a default if not... |
| getQualityMetricTemplate | Fills a MzQCqualityMetric object with id(accession) and name.... |
| getSyntaxValidator | Get a syntax validator for mzQC |
| hasFileSuffix | Checks if filepath ends in suffix (ignoring lower/upper case... |
| isUndefined | Tell if a variable's value is undefined (NA or NULL); If yes,... |
| isValidMzQC | Checks validity (= completeness) of mzQC objects - or lists... |
| localFileToURI | Convert a local filename, e.g. "./myData/test.mzML" to a... |
| 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... |
| MzQCcontrolledVocabulary | A controlled vocabulary document, usually pointing to an .obo... |
| MzQCcvParameter | A controlled vocabulary parameter, as detailed in the OBO... |
| MzQCDateTime | An mzQC-formatted date+time in ISO8601 format, as required by... |
| 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... |
| MzQCsetQuality | A setQuality object. Use it for metrics which are specific to... |
| NULL_to_charNA | Converts a NULL to NA_character_; or returns the argument... |
| NULL_to_NA | Converts a NULL to NA; or returns the argument unchanged... |
| 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... |
| removeFileSuffix | Removes the last suffix (including the last dot) from a... |
| removeIfExists | Remove a file, if it exists (useful for temporary files which... |
| rmzqc-package | rmzqc: Creation, Reading and Validation of 'mzqc' Files |
| toAnalysisSoftware | From an ID, e.g. "MS:1003162" (for PTX-QC), and some... |
| toQCMetric | Create an 'MzQCqualityMetric' object from two inputs (id and... |
| validateFromFile | Syntactically validates an mzQC document which is present as... |
| validateFromObj | Syntactically validates an mzQC document which is already in... |
| validateFromString | Syntactically validates an mzQC document which is already in... |
| writeMZQC | Writes a full mzQC object to disk. |
