Package: mzID 1.45.0
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:
mzID_1.45.0.tar.gz
mzID_1.45.0.zip(r-4.5)mzID_1.45.0.zip(r-4.4)mzID_1.45.0.zip(r-4.3)
mzID_1.45.0.tgz(r-4.4-any)mzID_1.45.0.tgz(r-4.3-any)
mzID_1.45.0.tar.gz(r-4.5-noble)mzID_1.45.0.tar.gz(r-4.4-noble)
mzID_1.45.0.tgz(r-4.4-emscripten)mzID_1.45.0.tgz(r-4.3-emscripten)
mzID.pdf |mzID.html✨
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-1.43.0(bioc 3.20)mzID-1.42.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
immunooncologydataimportmassspectrometryproteomics
Last updated 17 days agofrom:3c854c52ef. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 30 2024 |
| R-4.5-win | NOTE | Oct 30 2024 |
| R-4.5-linux | NOTE | Oct 30 2024 |
| R-4.4-win | NOTE | Oct 30 2024 |
| R-4.4-mac | NOTE | Oct 30 2024 |
| R-4.3-win | NOTE | Oct 30 2024 |
| R-4.3-mac | NOTE | Oct 30 2024 |
Exports:evidencefilesflattenididScanMapmzIDmzIDCollectionmzIDdatabasemzIDevidencemzIDparametersmzIDpeptidesmzIDpsmparametersremoveDecoysoftware
Dependencies:codetoolsdoParallelforeachiteratorsplyrProtGenericsRcppXML
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| A parser for the mzIdentML file format | mzID-package |
| Flatten an mzID related class into a table | flatten flatten,mzID-method flatten,mzIDCollection-method flatten,mzIDpeptides-method flatten,mzIDpsm-method |
| Parse an mzIdentML file | mzID |
| A class to contain data from mzIdentML-files | c,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 data | evidence files id idScanMap mzID-getters parameters software |
| Create a new mzIDCollection | mzIDCollection |
| A class to handle a set of mzID objects | as.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 class | mzIDdatabase |
| A class to store database information from an mzIdentML file | database,mzIDdatabase-method length,mzIDdatabase-method mzIDdatabase-class show,mzIDdatabase-method |
| A constructor for the mzIDevidence class | mzIDevidence |
| A class to store peptide evidence information from an mzIdentML file | evidence,mzIDevidence-method length,mzIDevidence-method mzIDevidence-class show,mzIDevidence-method |
| A constructor for the mzIDparameters class | mzIDparameters |
| A Class to store analysis information from the mzIdentML file | files,mzIDparameters-method length,mzIDparameters-method mzIDparameters-class parameters,mzIDparameters-method show,mzIDparameters-method software,mzIDparameters-method |
| A constructor for the mzIDpeptides class | mzIDpeptides |
| A class to store peptide information from an mzIdentML file | length,mzIDpeptides-method modifications,mzIDpeptides-method mzIDpeptides-class peptides,mzIDpeptides-method show,mzIDpeptides-method |
| A constructor for the mzIDpsm class | mzIDpsm |
| A class to store psm information from an mzIdentML file | id,mzIDpsm-method idScanMap,mzIDpsm-method length,mzIDpsm-method mzIDpsm-class scans,mzIDpsm-method show,mzIDpsm-method |
| Remove decoy identification | removeDecoy |
