mzID: An mzIdentML parser for R
Version 1.14.0

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.

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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)
Version1.14.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("mzID")

Man pages

flatten: Flatten an mzID related class into a table
increment: Tools to handle generation of lookup names for the dictionary
keyFor: Tools to handle generation of lookup names for the dictionary
mzID: Parse an mzIdentML file
mzID-class: A class to contain data from mzIdentML-files
mzIDCollection: Create a new mzIDCollection
mzIDCollection-class: A class to handle a set of mzID objects
mzIDdatabase: A constructor for the mzIDdatabase class
mzIDdatabase-class: A class to store database information from an mzIdentML file
mzIDevidence: A constructor for the mzIDevidence class
mzIDevidence-class: A class to store peptide evidence information from an...
mzID-getters: Getter functions for identification data
mzID-package: A parser for the mzIdentML file format
mzIDparameters: A constructor for the mzIDparameters class
mzIDparameters-class: A Class to store analysis information from the mzIdentML file
mzIDpeptides: A constructor for the mzIDpeptides class
mzIDpeptides-class: A class to store peptide information from an mzIdentML file
mzIDpsm: A constructor for the mzIDpsm class
mzIDpsm-class: A class to store psm information from an mzIdentML file
removeDecoy: Remove decoy identification

Functions

[,mzIDCollection,character,missing,missing-method Man page
[,mzIDCollection,logical,missing,missing-method Man page
[,mzIDCollection,numeric,missing,missing-method Man page
[[,mzIDCollection,character,missing-method Man page
[[,mzIDCollection,numeric,missing-method Man page
as.list.mzIDCollection Man page Source code
attrExtract Source code
attrExtractNameValuePair Source code
c,mzID-method Man page
c,mzIDCollection-method Man page
colNamesToLower Source code
countChildren Source code
database,mzID-method Man page
database,mzIDCollection-method Man page
database,mzIDdatabase-method Man page
evidence Man page
evidence,mzID-method Man page
evidence,mzIDCollection-method Man page
evidence,mzIDevidence-method Man page
files Man page
files,mzID-method Man page
files,mzIDCollection-method Man page
files,mzIDparameters-method Man page
flatten Man page
flatten,mzID-method Man page
flatten,mzIDCollection-method Man page
flatten,mzIDpeptides-method Man page
flatten,mzIDpsm-method Man page
getAdditionalPar Source code
getDatabaseFile Source code
getDatabaseFilter Source code
getDatabaseTranslation Source code
getEnzymes Source code
getFragmentTolerance Source code
getMassTable Source code
getModifications Source code
getParentTolerance Source code
getPath Source code
getRawFile Source code
getSearchType Source code
getSoftware Source code
getThreshold Source code
getVersion Source code
id Man page
id,mzID-method Man page
id,mzIDCollection-method Man page
id,mzIDpsm-method Man page
idScanMap Man page
idScanMap,mzID-method Man page
idScanMap,mzIDCollection-method Man page
idScanMap,mzIDpsm-method Man page
increment Man page
increment,mzIDCollection-method Man page
isRemote Source code
keyFor Man page
keyFor,mzIDCollection,character-method Man page
length,mzID-method Man page
length,mzIDCollection-method Man page
length,mzIDdatabase-method Man page
length,mzIDevidence-method Man page
length,mzIDparameters-method Man page
length,mzIDpeptides-method Man page
length,mzIDpsm-method Man page
modifications,mzID-method Man page
modifications,mzIDCollection-method Man page
modifications,mzIDpeptides-method Man page
mzID Man page Source code
mzID-class Man page
mzID-getters Man page
mzID-package Man page
mzIDCollection Man page Source code
mzIDCollection-class Man page
mzIDdatabase Man page Source code
mzIDdatabase-class Man page
mzIDevidence Man page Source code
mzIDevidence-class Man page
mzIDparameters Man page Source code
mzIDparameters-class Man page
mzIDpeptides Man page Source code
mzIDpeptides-class Man page
mzIDpsm Man page Source code
mzIDpsm-class Man page
names,mzIDCollection-method Man page
names<-,mzIDCollection,character-method Man page
parameters Man page
parameters,mzID-method Man page
parameters,mzIDCollection-method Man page
parameters,mzIDparameters-method Man page
peptides,mzID-method Man page
peptides,mzIDCollection-method Man page
peptides,mzIDpeptides-method Man page
prepareXML Source code
removeDecoy Man page
removeDecoy,mzID-method Man page
removeDecoy,mzIDCollection-method Man page
safeCol Source code
scans,mzID-method Man page
scans,mzIDCollection-method Man page
scans,mzIDpsm-method Man page
show,mzID-method Man page
show,mzIDCollection-method Man page
show,mzIDdatabase-method Man page
show,mzIDevidence-method Man page
show,mzIDparameters-method Man page
show,mzIDpeptides-method Man page
show,mzIDpsm-method Man page
software Man page
software,mzID-method Man page
software,mzIDCollection-method Man page
software,mzIDparameters-method Man page
subsetWithMapping Source code
type.convert Source code

Files

.travis.yml
DESCRIPTION
NAMESPACE
NEWS
R
R/aaa.R
R/generics.R
R/mzID-constructor.R
R/mzID-package.R
R/mzID.R
R/mzIDCollection.R
R/mzIDdatabase.R
R/mzIDevidence.R
R/mzIDparameters.R
R/mzIDpeptides.R
R/mzIDpsm.R
README.md
build
build/vignette.rds
inst
inst/doc
inst/doc/HOWTO_mzID.R
inst/doc/HOWTO_mzID.Rnw
inst/doc/HOWTO_mzID.pdf
inst/extdata
inst/extdata/55merge_omssa.mzid
inst/extdata/55merge_tandem.mzid
inst/extdata/MPC_example_Multiple_search_engines.mzid
inst/extdata/Mascot_MSMS_example.mzid
inst/extdata/Mascot_MSMS_example1.0.mzid
inst/extdata/Mascot_NA_example.mzid
inst/extdata/Mascot_top_down_example.mzid
inst/extdata/Sequest_example_ver1.1.mzid
inst/extdata/mascot_pmf_example.mzid
inst/extdata/testfile.xml
inst/tests
man
man/flatten.Rd
man/increment.Rd
man/keyFor.Rd
man/mzID-class.Rd
man/mzID-getters.Rd
man/mzID-package.Rd
man/mzID.Rd
man/mzIDCollection-class.Rd
man/mzIDCollection.Rd
man/mzIDdatabase-class.Rd
man/mzIDdatabase.Rd
man/mzIDevidence-class.Rd
man/mzIDevidence.Rd
man/mzIDparameters-class.Rd
man/mzIDparameters.Rd
man/mzIDpeptides-class.Rd
man/mzIDpeptides.Rd
man/mzIDpsm-class.Rd
man/mzIDpsm.Rd
man/removeDecoy.Rd
tests
tests/test-all.R
tests/testthat
tests/testthat/test-attrExtract.R
tests/testthat/test-attrExtractNameValuePair.R
tests/testthat/test-countChildren.R
tests/testthat/test-getPath.R
tests/testthat/test-getVersion.R
tests/testthat/test-isRemote.R
vignettes
vignettes/HOWTO_mzID.Rnw
mzID documentation built on May 20, 2017, 9:22 p.m.