Package: mzR 2.47.0

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:Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer

mzR_2.47.0.tar.gz
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mzR_2.47.0.tgz(r-4.6-x86_64)mzR_2.47.0.tgz(r-4.6-arm64)mzR_2.47.0.tgz(r-4.5-x86_64)mzR_2.47.0.tgz(r-4.5-arm64)
mzR_2.47.0.tar.gz(r-4.7-arm64)mzR_2.47.0.tar.gz(r-4.7-x86_64)mzR_2.47.0.tar.gz(r-4.6-arm64)mzR_2.47.0.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
card.svg |card.png
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

Uses libs:
  • curl– Easy-to-use client-side URL transfer library
  • openssl– Secure Sockets Layer toolkit
  • c++– GNU Standard C++ Library v3

On BioConductor:mzR-2.47.0(bioc 3.24)mzR-2.46.0(bioc 3.23)

immunooncologyinfrastructuredataimportproteomicsmetabolomicsmassspectrometrycurlopensslcpp

12.79 score 46 stars 46 packages 247 scripts 6.8k downloads 12 mentions 40 exports 10 dependencies

Last updated from:a438fe81b9. Checks:12 WARNING, 1 OK, 1 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING459
linux-devel-arm64WARNING809
linux-devel-x86_64WARNING851
source / vignettesOK652
linux-release-arm64WARNING783
linux-release-x86_64WARNING875
macos-release-arm64WARNING622
macos-release-x86_64WARNING1207
macos-oldrel-arm64WARNING699
macos-oldrel-x86_64WARNING1052
windows-develWARNING1353
windows-releaseWARNING1394
windows-oldrelWARNING1295
wasm-releaseFAIL171

Exports:analyzerchromatogramchromatogramHeaderchromatogramschromatogramsInfoclosecopyWriteMSDatadatabasedetectorenzymesfileNameget3DmapheaderinstrumentInfoionisationisInitializedisolationWindowmanufacturermodelmodificationsmzidInfonChromopenIDfileopenMSfileparapeakspeaksCountpsmspwiz.versionrunInfosampleInfoscoresoftwareInfosourceInfospecParamsspectrasubstitutionstictolerancewriteMSData

Dependencies:BiobaseBiocGenericsbiocmakedir.expiryfilelockgenericsncdf4ProtGenericsRcppRhdf5lib

A parser for raw and identification mass-spectrometry data

Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou

Rendered frommzR.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2026-03-18
Started: 2017-11-19

Readme and manuals

Help Manual

Help pageTopics
Write MS spectrum data to a MS file copying metadata from the originating filecopyWriteMSData
Returns the ion selection isolation windowisolationWindow 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-classesanalyzer,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 filewriteMSData writeMSData,list,character-method