Package: mzR 2.39.0
Steffen Neumann
mzR: parser for netCDF, mzXML and mzML and mzIdentML files (mass spectrometry data)
mzR provides a unified API to the common file formats and parsers available for mass spectrometry data. It comes with a subset of the proteowizard library for mzXML, mzML and mzIdentML. The netCDF reading code has previously been used in XCMS.
Authors:
mzR_2.39.0.tar.gz
mzR_2.39.0.zip(r-4.5)mzR_2.39.0.zip(r-4.4)mzR_2.39.0.zip(r-4.3)
mzR_2.39.0.tgz(r-4.4-arm64)mzR_2.39.0.tgz(r-4.4-x86_64)mzR_2.39.0.tgz(r-4.3-arm64)mzR_2.39.0.tgz(r-4.3-x86_64)
mzR_2.39.0.tar.gz(r-4.5-noble)mzR_2.39.0.tar.gz(r-4.4-noble)
mzR.pdf |mzR.html✨
mzR/json (API)
NEWS
| # Install 'mzR' in R: |
| install.packages('mzR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/sneumann/mzr/issues
On BioConductor:mzR-2.39.0(bioc 3.20)mzR-2.38.0(bioc 3.19)
Last updated 2 months agofrom:b2b8884387
Exports:analyzerchromatogramchromatogramHeaderchromatogramschromatogramsInfoclosecopyWriteMSDatadatabasedetectorenzymesfileNameget3DmapheaderinstrumentInfoionisationisInitializedisolationWindowmanufacturermodelmodificationsmzidInfonChromopenIDfileopenMSfileparapeakspeaksCountpsmspwiz.versionrunInfosampleInfoscoresoftwareInfosourceInfospecParamsspectrasubstitutionstictolerancewriteMSData
Dependencies:BiobaseBiocGenericsncdf4ProtGenericsRcppRhdf5lib
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Write MS spectrum data to a MS file copying metadata from the originating file | copyWriteMSData |
| Returns the ion selection isolation window | isolationWindow isolationWindow,character-method isolationWindow,mzRpwiz-method isolationWindow-methods |
| Access the metadata from an 'mzR' object. | analyzer chromatogramsInfo database detector enzymes instrumentInfo ionisation manufacturer model modifications mzidInfo para psms runInfo sampleInfo score softwareInfo sourceInfo specParams substitutions tolerance |
| Class 'mzR' and sub-classes | analyzer,mzRnetCDF-method analyzer,mzRpwiz-method chromatogramsInfo,mzRpwiz-method class:mzR class:mzRident class:mzRnetCDF class:mzRpwiz close close,mzRnetCDF-method close,mzRpwiz-method database,mzRident-method detector,mzRnetCDF-method detector,mzRpwiz-method enzymes,mzRident-method fileName,mzR-method instrumentInfo,mzRnetCDF-method instrumentInfo,mzRpwiz-method ionisation,mzRnetCDF-method ionisation,mzRpwiz-method isInitialized,mzRnetCDF-method length length,mzRident-method length,mzRnetCDF-method length,mzRpwiz-method manufacturer,mzRnetCDF-method manufacturer,mzRpwiz-method model,mzRnetCDF-method model,mzRpwiz-method modifications,mzRident-method mzidInfo,mzRident-method mzR-class mzRident-class mzRnetCDF-class mzRpwiz-class para,mzRident-method psms,mzRident-method runInfo,mzRnetCDF-method runInfo,mzRpwiz-method sampleInfo,mzRpwiz-method score,mzRident-method softwareInfo,mzRident-method softwareInfo,mzRpwiz-method sourceInfo,mzRident-method sourceInfo,mzRpwiz-method specParams,mzRident-method substitutions,mzRident-method tolerance,mzRident-method |
| Create and check mzR objects from netCDF, mzXML or mzML files. | fileName isInitialized openIDfile openMSfile |
| Access the raw data from an 'mzR' object. | chromatogram chromatogram,mzRnetCDF-method chromatogram,mzRpwiz-method chromatogramHeader chromatogramHeader,mzRnetCDF-method chromatogramHeader,mzRpwiz-method chromatograms chromatograms,mzRnetCDF-method chromatograms,mzRpwiz-method get3Dmap get3Dmap,mzRpwiz-method header header,mzRnetCDF,missing-method header,mzRnetCDF,numeric-method header,mzRpwiz,missing-method header,mzRpwiz,numeric-method nChrom peaks peaks,mzRnetCDF-method peaks,mzRpwiz-method peaksCount peaksCount,mzRpwiz,missing-method peaksCount,mzRpwiz,numeric-method spectra spectra,mzRnetCDF-method spectra,mzRpwiz-method tic tic,mzRpwiz-method |
| Get the version number of pwiz backend. | pwiz.version |
| Write MS spectrum data to an MS file | writeMSData writeMSData,list,character-method |
