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
mzR_2.47.0.zip(r-4.7)mzR_2.47.0.zip(r-4.6)mzR_2.47.0.zip(r-4.5)
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)
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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-2.47.0(bioc 3.24)mzR-2.46.0(bioc 3.23)

immunooncology infrastructure dataimport proteomics metabolomics massspectrometry curl openssl cpp

11.96 score 46 stars 46 packages 247 scripts 12 mentions 40 exports 10 dependencies

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

Target	Result	Time
bioc-checks	WARNING	470
linux-devel-arm64	WARNING	790
linux-devel-x86_64	WARNING	877
source / vignettes	OK	950
linux-release-arm64	WARNING	943
linux-release-x86_64	WARNING	873
macos-release-arm64	WARNING	1270
macos-release-x86_64	WARNING	2510
macos-oldrel-arm64	WARNING	681
macos-oldrel-x86_64	WARNING	1196
windows-devel	WARNING	1490
windows-release	WARNING	1330
windows-oldrel	WARNING	1895
wasm-release	FAIL	402

Exports:analyzer chromatogram chromatogramHeader chromatograms chromatogramsInfo close copyWriteMSData database detector enzymes fileName get3Dmap header instrumentInfo ionisation isInitialized isolationWindow manufacturer model modifications mzidInfo nChrom openIDfile openMSfile para peaks peaksCount psms pwiz.version runInfo sampleInfo score softwareInfo sourceInfo specParams spectra substitutions tic tolerance writeMSData

Dependencies:Biobase BiocGenerics biocmake dir.expiry filelock generics ncdf4 ProtGenerics Rcpp Rhdf5lib

A parser for raw and identification mass-spectrometry data

Rendered frommzR.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

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