Package index • rmzqc

All functions

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-class MzQCanalysisSoftware: Details of the software used to create the QC metrics

MzQCbaseQuality-class MzQCbaseQuality: Base class of runQuality/setQuality

MzQCbaseQuality_getMetric: Extract a certain metric from a runQuality's list of MzQCqualityMetric

MzQCcontrolledVocabulary-class MzQCcontrolledVocabulary: A controlled vocabulary document, usually pointing to an .obo file

MzQCcvParameter-class MzQCcvParameter: A controlled vocabulary parameter, as detailed in the OBO file

MzQCDateTime-class MzQCDateTime: An mzQC-formatted date+time in ISO8601 format, as required by the mzQC spec doc.

MzQCinputFile-class MzQCinputFile: An inputfile within metadata for a run/setQuality

MzQCmetadata-class MzQCmetadata: The metadata for a run/setQuality

MzQCmzQC-class MzQCmzQC: Root element of an mzQC document

MzQCqualityMetric-class MzQCqualityMetric: The central class to store QC information

MzQCrunQuality-class MzQCrunQuality: A runQuality object. Use to report metrics for individual runs which are independent of other runs.

MzQCsetQuality-class 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).

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.