Creation, Reading and Validation of 'mzqc' Files
Check if a field exists in data and warn if it doesn't, then return th...
Checks the value's class type, which should match at least of the type...
Check for unexpected fields in data and warn if any are found
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
Get an optional value from data, using a default if not present
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 variable's value is undefined (NA or NULL); If yes, and it i...
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
Extract a certain metric from a runQuality's list of MzQCqualityMetric
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
Read a JSON object 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.