tests/testthat/_snaps/io.md

In rmzqc: Creation, Reading and Validation of 'mzqc' Files

readMZQC and writeMZQC - check for extra data in mzQC file and warn

Code
  readMZQCFromJSON(json_raw)
Condition
  Warning:
  Unexpected field(s) found in data for class 'MzQCmzQC' in MzQCmzQC: newData
  Warning:
  Unexpected field(s) found in data for class 'MzQCmetadata': stuff
  Warning:
  Unexpected field(s) found in data for class 'MzQCmetadata' in MzQCmzQC$runQualities[1]$metadata: stuff
Output
  Reference class object of class "MzQCmzQC"
  Field "version":
  [1] "1.0.0"
  Field "creationDate":
  Reference class object of class "MzQCDateTime"
  Field "datetime":
  [1] "2022-10-17T00:00:00Z"
  Field "contactName":
  [1] "bielow"
  Field "contactAddress":
  [1] "[e-mail]"
  Field "description":
  [1] "A minimal mzQC test document with bogus data"
  Field "runQualities":
  [[1]]
  Reference class object of class "MzQCrunQuality"
  Field "metadata":
  Reference class object of class "MzQCmetadata"
  Field "label":
  [1] "file:///c:/data/special.raw"
  Field "inputFiles":
  [[1]]
  Reference class object of class "MzQCinputFile"
  Field "name":
  [1] "special.raw"
  Field "location":
  [1] "file:///c:/data/special.raw"
  Field "fileFormat":
  Reference class object of class "MzQCcvParameter"
  Field "accession":
  [1] "MS:1000563"
  Field "name":
  [1] "Thermo RAW format"
  Field "value":
  [1] NA
  Field "description":
  [1] NA
  Field "fileProperties":
  list()

  Field "analysisSoftware":
  [[1]]
  Reference class object of class "MzQCanalysisSoftware"
  Field "accession":
  [1] "MS:1003162"
  Field "name":
  [1] "PTX-QC"
  Field "version":
  [1] "1.0.13"
  Field "uri":
  [1] "https://github.com/cbielow/PTXQC/"
  Field "description":
  [1] "\"Proteomics (PTX) - QualityControl (QC) software for QC report generation and visualization.\" [DOI:10.1021/acs.jproteome.5b00780, PMID:26653327, https://github.com/cbielow/PTXQC/]"
  Field "value":
  [1] NA

  Field "cvParameters":
  list()
  Field "qualityMetrics":
  [[1]]
  Reference class object of class "MzQCqualityMetric"
  Field "accession":
  [1] "MS:4000059"
  Field "name":
  [1] "number of MS1 spectra"
  Field "description":
  [1] "\"The number of MS1 events in the run.\" [PSI:MS]"
  Field "value":
  [1] 13405
  Field "unit":
  list()


  Field "setQualities":
  list()
  Field "controlledVocabularies":
  [[1]]
  Reference class object of class "MzQCcontrolledVocabulary"
  Field "name":
  [1] "Proteomics Standards Initiative Mass Spectrometry Ontology"
  Field "uri":
  [1] "https://github.com/HUPO-PSI/psi-ms-CV/releases/download/v4.1.95/psi-ms.obo"
  Field "version":
  [1] "4.1.95"

rmzqc documentation built on June 8, 2025, 1:59 p.m.