Package: mzR 2.47.1

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_2.47.1.tar.gz
mzR_2.47.1.zip(r-4.7-x86_64)mzR_2.47.1.zip(r-4.7-arm64)mzR_2.47.1.zip(r-4.6-x86_64)mzR_2.47.1.zip(r-4.6-arm64)mzR_2.47.1.zip(r-4.5-x86_64)
mzR_2.47.1.tgz(r-4.6-x86_64)mzR_2.47.1.tgz(r-4.6-arm64)mzR_2.47.1.tgz(r-4.5-x86_64)mzR_2.47.1.tgz(r-4.5-arm64)
mzR_2.47.1.tar.gz(r-4.7-arm64)mzR_2.47.1.tar.gz(r-4.7-x86_64)mzR_2.47.1.tar.gz(r-4.6-arm64)mzR_2.47.1.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
mzR/json (API)

# 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-2.47.1(bioc 3.24)mzR-2.46.0(bioc 3.23)

immunooncologyinfrastructuredataimportproteomicsmetabolomicsmassspectrometrycurlopensslcpp

11.59 score 44 stars 54 packages 263 scripts 8.6k downloads 12 mentions 40 exports 10 dependencies

Last updated from:cb68fe308a. Checks:1 WARNING, 14 ERROR, 1 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING493
linux-devel-arm64ERROR611
linux-devel-x86_64ERROR878
source / vignettesERROR708
linux-release-arm64ERROR596
linux-release-x86_64ERROR600
macos-release-arm64ERROR745
macos-release-x86_64ERROR1355
macos-oldrel-arm64ERROR753
macos-oldrel-x86_64ERROR1141
windows-devel-arm64ERROR1016
windows-devel-x86_64ERROR1103
windows-release-arm64ERROR1037
windows-release-x86_64ERROR770
windows-oldrel-x86_64ERROR859
wasm-releaseFAIL161

Exports:analyzerchromatogramchromatogramHeaderchromatogramschromatogramsInfoclosecopyWriteMSDatadatabasedetectorenzymesfileNameget3DmapheaderinstrumentInfoionisationisInitializedisolationWindowmanufacturermodelmodificationsmzidInfonChromopenIDfileopenMSfileparapeakspeaksCountpsmspwiz.versionrunInfosampleInfoscoresoftwareInfosourceInfospecParamsspectrasubstitutionstictolerancewriteMSData

Dependencies:BiobaseBiocGenericsbiocmakedir.expiryfilelockgenericsncdf4ProtGenericsRcppRhdf5lib

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