Creation, Reading and Validation of 'mzqc' Files


[Up] [Top]

Documentation for package ‘rmzqc’ version 0.1.0

Help Pages

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.