R: Creation, Reading and Validation of 'mzqc' Files

# Creation, Reading and Validation of 'mzqc' Files

## Documentation for package ‘rmzqc’ version 0.7.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## 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_ | 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 variable's value is undefined (NA or NULL); If yes, and it is 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
MzQCbaseQuality_getMetric | Extract a certain metric from a runQuality's list of MzQCqualityMetric
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
readMZQCFromJSON | Read a JSON object 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.