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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("mzID")
AuthorThomas Lin Pedersen, Vladislav A Petyuk with contributions from Laurent Gatto and Sebastian Gibb.
Bioconductor views DataImport MassSpectrometry Proteomics
Date of publicationNone
MaintainerThomas Lin Pedersen <thomasp85@gmail.com>
LicenseGPL (>= 2)
Version1.12.0

View on Bioconductor

Functions

as.list.mzIDCollection Man page
c,mzIDCollection-method Man page
c,mzID-method Man page
database,mzIDCollection-method Man page
database,mzIDdatabase-method Man page
database,mzID-method Man page
evidence Man page
evidence,mzIDCollection-method Man page
evidence,mzIDevidence-method Man page
evidence,mzID-method Man page
files Man page
files,mzIDCollection-method Man page
files,mzID-method Man page
files,mzIDparameters-method Man page
flatten Man page
flatten,mzIDCollection-method Man page
flatten,mzID-method Man page
flatten,mzIDpeptides-method Man page
flatten,mzIDpsm-method Man page
id Man page
id,mzIDCollection-method Man page
id,mzID-method Man page
id,mzIDpsm-method Man page
idScanMap Man page
idScanMap,mzIDCollection-method Man page
idScanMap,mzID-method Man page
idScanMap,mzIDpsm-method Man page
increment Man page
increment,mzIDCollection-method Man page
keyFor Man page
keyFor,mzIDCollection,character-method Man page
length,mzIDCollection-method Man page
length,mzIDdatabase-method Man page
length,mzIDevidence-method Man page
length,mzID-method Man page
length,mzIDparameters-method Man page
length,mzIDpeptides-method Man page
length,mzIDpsm-method Man page
modifications,mzIDCollection-method Man page
modifications,mzID-method Man page
modifications,mzIDpeptides-method Man page
mzID Man page
mzID-class Man page
mzIDCollection Man page
[[,mzIDCollection,character,missing-method Man page
[,mzIDCollection,character,missing,missing-method Man page
mzIDCollection-class Man page
[,mzIDCollection,logical,missing,missing-method Man page
[[,mzIDCollection,numeric,missing-method Man page
[,mzIDCollection,numeric,missing,missing-method Man page
mzIDdatabase Man page
mzIDdatabase-class Man page
mzIDevidence Man page
mzIDevidence-class Man page
mzID-getters Man page
mzID-package Man page
mzIDparameters Man page
mzIDparameters-class Man page
mzIDpeptides Man page
mzIDpeptides-class Man page
mzIDpsm Man page
mzIDpsm-class Man page
names<-,mzIDCollection,character-method Man page
names,mzIDCollection-method Man page
parameters Man page
parameters,mzIDCollection-method Man page
parameters,mzID-method Man page
parameters,mzIDparameters-method Man page
peptides,mzIDCollection-method Man page
peptides,mzID-method Man page
peptides,mzIDpeptides-method Man page
removeDecoy Man page
removeDecoy,mzIDCollection-method Man page
removeDecoy,mzID-method Man page
scans,mzIDCollection-method Man page
scans,mzID-method Man page
scans,mzIDpsm-method Man page
show,mzIDCollection-method Man page
show,mzIDdatabase-method Man page
show,mzIDevidence-method Man page
show,mzID-method Man page
show,mzIDparameters-method Man page
show,mzIDpeptides-method Man page
show,mzIDpsm-method Man page
software Man page
software,mzIDCollection-method Man page
software,mzID-method Man page
software,mzIDparameters-method Man page

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.