Package: mzR 2.41.1

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_2.41.1.tar.gz
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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'))

Peer review:

Bug tracker:https://github.com/sneumann/mzr/issues

Uses libs:
  • zlib– Compression library
  • c++– GNU Standard C++ Library v3

On BioConductor:mzR-2.41.0(bioc 3.21)mzR-2.40.0(bioc 3.20)

immunooncologyinfrastructuredataimportproteomicsmetabolomicsmassspectrometry

12.62 score 42 stars 43 packages 188 scripts 5.6k downloads 12 mentions 40 exports 7 dependencies

Last updated 2 days agofrom:0368dbf558. Checks:OK: 1 WARNING: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 20 2024
R-4.5-win-x86_64WARNINGNov 20 2024
R-4.5-linux-x86_64WARNINGNov 20 2024
R-4.4-win-x86_64WARNINGNov 20 2024
R-4.4-mac-x86_64WARNINGNov 20 2024
R-4.4-mac-aarch64WARNINGNov 20 2024
R-4.3-win-x86_64WARNINGNov 20 2024
R-4.3-mac-x86_64WARNINGNov 20 2024
R-4.3-mac-aarch64WARNINGNov 20 2024

Exports:analyzerchromatogramchromatogramHeaderchromatogramschromatogramsInfoclosecopyWriteMSDatadatabasedetectorenzymesfileNameget3DmapheaderinstrumentInfoionisationisInitializedisolationWindowmanufacturermodelmodificationsmzidInfonChromopenIDfileopenMSfileparapeakspeaksCountpsmspwiz.versionrunInfosampleInfoscoresoftwareInfosourceInfospecParamsspectrasubstitutionstictolerancewriteMSData

Dependencies:BiobaseBiocGenericsgenericsncdf4ProtGenericsRcppRhdf5lib

A parser for raw and identification mass-spectrometry data

Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou

Rendered frommzR.Rmdusingknitr::rmarkdownon Nov 20 2024.

Last update: 2024-02-24
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