check_type |
Checks the value's class type, which should match at least of the types given in any_expected_class_types. |
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) |
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 to mzQC objects |
getCVDictionary |
Parse the content of 'psi-ms.obo', 'pato.obo', and 'uo.obo' from the 'rmzqc/cv/' folder as ontology and return their union |
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. |
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 |
MzQCanalysisSoftware |
Details of the software used to create the QC metrics |
MzQCanalysisSoftware-class |
Details of the software used to create the QC metrics |
MzQCbaseQuality |
Base class of runQuality/setQuality |
MzQCbaseQuality-class |
Base class of runQuality/setQuality |
MzQCcontrolledVocabulary |
A controlled vocabulary document, usually pointing to an .obo file |
MzQCcontrolledVocabulary-class |
A controlled vocabulary document, usually pointing to an .obo file |
MzQCcvParameter |
A controlled vocabulary parameter, as detailed in the OBO file |
MzQCcvParameter-class |
A controlled vocabulary parameter, as detailed in the OBO file |
MzQCDateTime |
An mzQC-formatted date+time in ISO8601 format, as required by the mzQC spec doc. |
MzQCDateTime-class |
An mzQC-formatted date+time in ISO8601 format, as required by the mzQC spec doc. |
MzQCinputFile |
An inputfile within metadata for a run/setQuality |
MzQCinputFile-class |
An inputfile within metadata for a run/setQuality |
MzQCmetadata |
The metadata for a run/setQuality |
MzQCmetadata-class |
The metadata for a run/setQuality |
MzQCmzQC |
Root element of an mzQC document |
MzQCmzQC-class |
Root element of an mzQC document |
MzQCqualityMetric |
The central class to store QC information |
MzQCqualityMetric-class |
The central class to store QC information |
MzQCrunQuality |
A runQuality object. Use to report metrics for individual runs which are independent of other runs. |
MzQCrunQuality-class |
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). |
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_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. |
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 |
writeMZQC |
Writes a full mzQC object to disk. |