Creation, Reading and Validation of 'mzqc' Files
Checks the value's class type, which should match at least of the type...
CV_
For a given filename (e.g. "test.mzML"), check the suffix and translat...
Allow conversion of plain named lists of R objects (from jSON) to mzQC...
Allow conversion of a plain R object (obtained from jSON) to an mzQC o...
Fetch and parse the 'psi-ms.obo' and some metadata from the usual sour...
Returns an MzQCcontrolledVocabulary for the currently used CV (see `...
Returns the CV singleton. See CV_.
Fills a MzQCcvParameter object with id(accession) and name. The value ...
Returns an MzQCcontrolledVocabulary for the currently used CV (see `ge...
Get the latest PSI-MS CV release URL
Obtains the 'data-version' from a local (i.e. non-url) PSI-MS-CV
Fills a MzQCqualityMetric object with id(accession) and name. The valu...
Get a syntax validator for mzQC
Checks if filepath ends in suffix (ignoring lower/upper case differenc...
Tell if a string is undefined (NA or NULL); If yes, and its required b...
Checks validity (= completeness) of mzQC objects - or lists (JSON arra...
Convert a local filename, e.g. "./myData/test.mzML" to a proper URI (e...
Details of the software used to create the QC metrics
Base class of runQuality/setQuality
A controlled vocabulary document, usually pointing to an .obo file
A controlled vocabulary parameter, as detailed in the OBO file
An mzQC-formatted date+time in ISO8601 format, as required by the mzQC...
An inputfile within metadata for a run/setQuality
The metadata for a run/setQuality
Root element of an mzQC document
The central class to store QC information
A runQuality object. Use to report metrics for individual runs which a...
A setQuality object. Use it for metrics which are specific to sets, i....
Converts a NULL to NA_character_; or returns the argument unchanged ot...
Converts a NULL to NA; or returns the argument unchanged otherwise
Get the information of each CV term from an obo file.
Read a JSON file in mzQC format into an MzQCmzQC root object
Removes the last suffix (including the last dot) from a filename. If n...
Remove a file, if it exists (useful for temporary files which may or m...
rmzqc: Creation, Reading and Validation of 'mzqc' Files
From an ID, e.g. "MS:1003162" (for PTX-QC), and some additional inform...
Create an 'MzQCqualityMetric' object from two inputs (id and value).
Syntactically validates an mzQC document which is present as a file.
Syntactically validates an mzQC document which is already in memory as...
Syntactically validates an mzQC document which is already in memory as...
Writes a full mzQC object to disk.
Reads, writes and validates 'mzQC' files. The 'mzQC' format is a standardized file format for the exchange, transmission, and archiving of quality metrics derived from biological mass spectrometry data, as defined by the HUPO-PSI (Human Proteome Organisation - Proteomics Standards Initiative) Quality Control working group. See <https://hupo-psi.github.io/mzQC/> for details.