Package: mzID 1.51.0

Laurent Gatto

mzID: An mzIdentML parser for R

A parser for mzIdentML files implemented using the XML package. The parser tries to be general and able to handle all types of mzIdentML files with the drawback of having less 'pretty' output than a vendor specific parser. Please contact the maintainer with any problems and supply an mzIdentML file so the problems can be fixed quickly.

Authors:Laurent Gatto [ctb, cre], Thomas Pedersen [aut], Vladislav Petyuk [ctb]

mzID_1.51.0.tar.gz
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manual.pdf |manual.html✨
card.svg |card.png
mzID/json (API)
NEWS

# Install 'mzID' in R:
install.packages('mzID', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:mzID-1.51.0(bioc 3.24)mzID-1.50.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

immunooncologydataimportmassspectrometryproteomics

8.16 score 39 packages 38 scripts 5.5k downloads 4 mentions 15 exports 8 dependencies

Last updated from:61b447eeb1. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR141
linux-devel-x86_64NOTE152
source / vignettesOK183
linux-release-x86_64NOTE182
macos-release-arm64NOTE90
macos-oldrel-arm64NOTE102
windows-develNOTE82
windows-releaseNOTE86
windows-oldrelNOTE79
wasm-releaseOK99

Exports:evidencefilesflattenididScanMapmzIDmzIDCollectionmzIDdatabasemzIDevidencemzIDparametersmzIDpeptidesmzIDpsmparametersremoveDecoysoftware

Dependencies:codetoolsdoParallelforeachiteratorsplyrProtGenericsRcppXML

Using mzID

Rendered fromHOWTO_mzID.Rnwusingknitron May 30 2026.

Last update: 2016-04-21
Started: 2013-09-17

Readme and manuals

Help Manual

Help pageTopics
A parser for the mzIdentML file formatmzID-package
Flatten an mzID related class into a tableflatten flatten,mzID-method flatten,mzIDCollection-method flatten,mzIDpeptides-method flatten,mzIDpsm-method
Parse an mzIdentML filemzID
A class to contain data from mzIdentML-filesc,mzID-method database,mzID-method evidence,mzID-method files,mzID-method id,mzID-method idScanMap,mzID-method length,mzID-method modifications,mzID-method mzID-class parameters,mzID-method peptides,mzID-method removeDecoy,mzID-method scans,mzID-method show,mzID-method software,mzID-method
Getter functions for identification dataevidence files id idScanMap mzID-getters parameters software
Create a new mzIDCollectionmzIDCollection
A class to handle a set of mzID objectsas.list.mzIDCollection c,mzIDCollection-method database,mzIDCollection-method evidence,mzIDCollection-method files,mzIDCollection-method id,mzIDCollection-method idScanMap,mzIDCollection-method length,mzIDCollection-method modifications,mzIDCollection-method mzIDCollection-class names,mzIDCollection-method names<-,mzIDCollection,character-method parameters,mzIDCollection-method peptides,mzIDCollection-method removeDecoy,mzIDCollection-method scans,mzIDCollection-method show,mzIDCollection-method software,mzIDCollection-method [,mzIDCollection,character,missing,missing-method [,mzIDCollection,logical,missing,missing-method [,mzIDCollection,numeric,missing,missing-method [[,mzIDCollection,character,missing-method [[,mzIDCollection,numeric,missing-method
A constructor for the mzIDdatabase classmzIDdatabase
A class to store database information from an mzIdentML filedatabase,mzIDdatabase-method length,mzIDdatabase-method mzIDdatabase-class show,mzIDdatabase-method
A constructor for the mzIDevidence classmzIDevidence
A class to store peptide evidence information from an mzIdentML fileevidence,mzIDevidence-method length,mzIDevidence-method mzIDevidence-class show,mzIDevidence-method
A constructor for the mzIDparameters classmzIDparameters
A Class to store analysis information from the mzIdentML filefiles,mzIDparameters-method length,mzIDparameters-method mzIDparameters-class parameters,mzIDparameters-method show,mzIDparameters-method software,mzIDparameters-method
A constructor for the mzIDpeptides classmzIDpeptides
A class to store peptide information from an mzIdentML filelength,mzIDpeptides-method modifications,mzIDpeptides-method mzIDpeptides-class peptides,mzIDpeptides-method show,mzIDpeptides-method
A constructor for the mzIDpsm classmzIDpsm
A class to store psm information from an mzIdentML fileid,mzIDpsm-method idScanMap,mzIDpsm-method length,mzIDpsm-method mzIDpsm-class scans,mzIDpsm-method show,mzIDpsm-method
Remove decoy identificationremoveDecoy