mzID: An mzIdentML parser for R

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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.

Author
Thomas Lin Pedersen, Vladislav A Petyuk with contributions from Laurent Gatto and Sebastian Gibb.
Date of publication
None
Maintainer
Thomas Lin Pedersen <thomasp85@gmail.com>
License
GPL (>= 2)
Version
1.12.0

View on Bioconductor

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

Files in this package

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