Package: rmzqc 0.5.4

Chris Bielow

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

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.

Authors:Chris Bielow [aut, cre], David Jimenez-Morales [rev, ctb]

rmzqc_0.5.4.tar.gz
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rmzqc.pdf |rmzqc.html✨
rmzqc/json (API)
NEWS

# Install 'rmzqc' in R:
install.packages('rmzqc', repos = c('https://ms-quality-hub.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/ms-quality-hub/rmzqc/issues

On CRAN:

hacktoberfestmass-spectrometrymzqcquality-control

5.73 score 2 stars 3 packages 10 scripts 396 downloads 39 exports 62 dependencies

Last updated 7 months agofrom:c809b32518. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 12 2024
R-4.5-winOKNov 12 2024
R-4.5-linuxOKNov 12 2024
R-4.4-winOKNov 12 2024
R-4.4-macOKNov 12 2024
R-4.3-winOKNov 12 2024
R-4.3-macOKNov 12 2024

Exports:check_typeCV_filenameToCVfromDatatoMzQCfromDatatoMzQCobjgetCVDictionarygetCVInfogetCVSingletongetCVTemplategetDefaultCVgetLatest_PSICV_URLgetLocal_CV_VersiongetQualityMetricTemplatehasFileSuffixisUndefinedisValidMzQClocalFileToURIMzQCanalysisSoftwareMzQCbaseQualityMzQCcontrolledVocabularyMzQCcvParameterMzQCDateTimeMzQCinputFileMzQCmetadataMzQCmzQCMzQCqualityMetricMzQCrunQualityMzQCsetQualityNULL_to_charNANULL_to_NAreadMZQCremoveFileSuffixremoveIfExiststoAnalysisSoftwaretoQCMetricvalidateFromFilevalidateFromObjvalidateFromStringwriteMZQC

Dependencies:base64encbriobslibcachemcallrclicollectionscpp11crayoncurldescdiffobjdigestdplyrevaluatefansifastmapfontawesomefsgenericsgluehighrhtmltoolsjquerylibjsonlitejsonvalidateknitrlifecyclemagrittrmemoisemimeontologyIndexpillarpkgbuildpkgconfigpkgloadpraiseprocessxpspurrrR6R6PrappdirsRcpprlangrmarkdownrprojrootsassstringistringrtestthattibbletidyrtidyselecttinytexutf8V8vctrswaldowithrxfunyaml

Basic R-Usage Guide for rMZQC

Chris Bielow [email protected]

Rendered frombasic_guide.Rmdusingknitr::rmarkdownon Nov 12 2024.

Last update: 2024-04-16
Started: 2022-08-18

Using a custom controlled vocabulary for rMZQC

Chris Bielow [email protected]

Rendered fromusing_a_custom_cv.Rmdusingknitr::rmarkdownon Nov 12 2024.

Last update: 2023-08-05
Started: 2023-07-05

Validation of mzQC documents

Chris Bielow [email protected]

Rendered fromvalidation_guide.Rmdusingknitr::rmarkdownon Nov 12 2024.

Last update: 2022-10-28
Started: 2022-10-28

Readme and manuals

Help Manual

Help pageTopics
Checks the value's class type, which should match at least of the types given in any_expected_class_types.check_type
CV_CV_
For a given filename (e.g. "test.mzML"), check the suffix and translate it to an PSI-MS CV term, e.g. 'MS:1000584'filenameToCV
Allow conversion of plain named lists of R objects (from jSON) to mzQC objectsfromDatatoMzQC
Allow conversion of a plain R object (obtained from jSON) to an mzQC objectfromDatatoMzQCobj
Fetch and parse the 'psi-ms.obo' and some metadata from the usual sources to use as ontology.getCVDictionary
Returns an 'MzQCcontrolledVocabulary' for the currently used CV (see 'getCVSingleton') using 'getCVSingleton()$getData()$URI' and $version.getCVInfo
Returns the CV singleton. See 'CV_'.getCVSingleton
Fills a MzQCcvParameter object with id(accession) and name. The value (if any) needs to be set afterwards.getCVTemplate
Returns an MzQCcontrolledVocabulary for the currently used CV (see 'getCVSingleton')getDefaultCV
Get the latest PSI-MS CV release URLgetLatest_PSICV_URL
Obtains the 'data-version' from a local (i.e. non-url) PSI-MS-CVgetLocal_CV_Version
Fills a MzQCqualityMetric object with id(accession) and name. The value (if any) and unit (if any) need to be set afterwards.getQualityMetricTemplate
Get a syntax validator for mzQCgetSyntaxValidator
Checks if filepath ends in suffix (ignoring lower/upper case differences). If suffix does not start with a '.' it is prepended automatically.hasFileSuffix
Tell if a string is undefined (NA or NULL); If yes, and its required by the mzQC standard, we can raise an error.isUndefined
Checks validity (= completeness) of mzQC objects - or lists (JSON arrays) thereofisValidMzQC
Convert a local filename, e.g. "./myData/test.mzML" to a proper URI (e.g. "file:///user/bielow/myData/test.mzML")localFileToURI
Details of the software used to create the QC metricsMzQCanalysisSoftware MzQCanalysisSoftware-class
Base class of runQuality/setQualityMzQCbaseQuality MzQCbaseQuality-class
A controlled vocabulary document, usually pointing to an .obo fileMzQCcontrolledVocabulary MzQCcontrolledVocabulary-class
A controlled vocabulary parameter, as detailed in the OBO fileMzQCcvParameter MzQCcvParameter-class
An mzQC-formatted date+time in ISO8601 format, as required by the mzQC spec doc.MzQCDateTime MzQCDateTime-class
An inputfile within metadata for a run/setQualityMzQCinputFile MzQCinputFile-class
The metadata for a run/setQualityMzQCmetadata MzQCmetadata-class
Root element of an mzQC documentMzQCmzQC MzQCmzQC-class
The central class to store QC informationMzQCqualityMetric MzQCqualityMetric-class
A runQuality object. Use to report metrics for individual runs which are independent of other runs.MzQCrunQuality MzQCrunQuality-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).MzQCsetQuality MzQCsetQuality-class
Converts a NULL to NA_character_; or returns the argument unchanged otherwiseNULL_to_charNA
Converts a NULL to NA; or returns the argument unchanged otherwiseNULL_to_NA
Get the information of each CV term from an obo file.parseOBO
Read a JSON file in mzQC format into an MzQCmzQC root objectreadMZQC
Removes the last suffix (including the last dot) from a filename. If no dot exists, the full string is returned.removeFileSuffix
Remove a file, if it exists (useful for temporary files which may or may not have been created)removeIfExists
From an ID, e.g. "MS:1003162" (for PTX-QC), and some additional information, create an 'analysisSoftware' node for mzQCtoAnalysisSoftware
Create an 'MzQCqualityMetric' object from two inputstoQCMetric
Syntactically validates an mzQC document which is present as a file.validateFromFile
Syntactically validates an mzQC document which is already in memory as mzQC root object, as obtained by, e.g. readMZQC().validateFromObj
Syntactically validates an mzQC document which is already in memory as JSON string. e.g. the string "{ mzQC : {}}"validateFromString
Writes a full mzQC object to disk.writeMZQC