Creation, Reading and Validation of 'mzqc' Files

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Documentation for package ‘rmzqc’ version 0.5.5

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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 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.
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 (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.