MSGFplus: An interface between R and MS-GF+

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This package contains function to perform peptide identification using MS-GF+

Author
Thomas Lin Pedersen
Date of publication
None
Maintainer
Thomas Lin Pedersen <thomasp85@gmail.com>
License
GPL (>= 2)
Version
1.8.0

View on Bioconductor

Man pages

chargeRange
Get and set the charge range in msgfPar objects
db
Get and set database in msgfPar objects
enzyme
Get and set enzyme in msgfPar objects
fragmentation
Get and set fragmentation in msgfPar objects
getMSGFpar
Get a string representation of an msgfPar-related object
instrument
Get and set instrument in msgfPar objects
isotopeError
Get and set isotope error in msgfPar objects
lengthRange
Get and set peptide length range in msgfPar objects
matches
Get and set the number of matches in msgfPar objects
mods
Get and set the modifications in msgfPar objects
msgfAsync-class
A class referencing an asynchronous execution of MS-GF+
msgfPar
Constructor for the msgfPar class
msgfParChargeRange-class
A class handling charge ranges
msgfPar-class
A class to contain parameters used in an MS-GF+ analysis
msgfParEnzyme-class
A class handling enzyme selection
msgfParFragmentation-class
A class handling Fragmentation types
msgfParFromID
Extract parameters from mzIdentML result file
msgfParGUI
A simple GUI to create msgfPar objects
msgfParInstrument-class
A class handling instrument types
msgfParIsotopeError-class
A class handling isotope errors
msgfParLengthRange-class
A class handling length ranges
msgfParMatches-class
A class handling number of matches
msgfParModification-class
A class handling modification characteristics
msgfParModificationList-class
A class handling a list of modifications
msgfParNtt-class
A class handling cleavage specificity
msgfParProtocol-class
A class handling protocol choice
msgfParTda-class
A class handling use of target-decoy approach for FDR...
msgfParTolerance-class
A class handling parent ion tolerance
MSGFplus-package
An interface between R and MS-GF+
ntt
Get and set cleavage specificity in msgfPar objects
protocol
Get and set protocol in msgfPar objects
runMSGF
Runs MS-GF+ based on the given msgfPar object
tda
Get and set use of target-decoy approach in msgfPar objects
tolerance
Get and set the parent tolerance in msgfPar objects

Files in this package

MSGFplus/DESCRIPTION
MSGFplus/NAMESPACE
MSGFplus/NEWS
MSGFplus/R
MSGFplus/R/MSGFplus-package.R
MSGFplus/R/aaa.R
MSGFplus/R/generics.R
MSGFplus/R/msgfAsync.R
MSGFplus/R/msgfPar-getters.R
MSGFplus/R/msgfPar.R
MSGFplus/R/msgfParChargeRange.R
MSGFplus/R/msgfParEnzyme.R
MSGFplus/R/msgfParFragmentation.R
MSGFplus/R/msgfParGUI.R
MSGFplus/R/msgfParInstrument.R
MSGFplus/R/msgfParIsotopeError.R
MSGFplus/R/msgfParLengthRange.R
MSGFplus/R/msgfParMatches.R
MSGFplus/R/msgfParModification.R
MSGFplus/R/msgfParModificationList.R
MSGFplus/R/msgfParNtt.R
MSGFplus/R/msgfParProtocol.R
MSGFplus/R/msgfParTda.R
MSGFplus/R/msgfParTolerance.R
MSGFplus/R/zzz.R
MSGFplus/README.html
MSGFplus/README.md
MSGFplus/build
MSGFplus/build/vignette.rds
MSGFplus/inst
MSGFplus/inst/doc
MSGFplus/inst/doc/Using_MSGFplus.R
MSGFplus/inst/doc/Using_MSGFplus.Rmd
MSGFplus/inst/doc/Using_MSGFplus.html
MSGFplus/inst/extdata
MSGFplus/inst/extdata/milk-proteins.fasta
MSGFplus/man
MSGFplus/man/MSGFplus-package.Rd
MSGFplus/man/chargeRange.Rd
MSGFplus/man/db.Rd
MSGFplus/man/enzyme.Rd
MSGFplus/man/fragmentation.Rd
MSGFplus/man/getMSGFpar.Rd
MSGFplus/man/instrument.Rd
MSGFplus/man/isotopeError.Rd
MSGFplus/man/lengthRange.Rd
MSGFplus/man/matches.Rd
MSGFplus/man/mods.Rd
MSGFplus/man/msgfAsync-class.Rd
MSGFplus/man/msgfPar-class.Rd
MSGFplus/man/msgfPar.Rd
MSGFplus/man/msgfParChargeRange-class.Rd
MSGFplus/man/msgfParEnzyme-class.Rd
MSGFplus/man/msgfParFragmentation-class.Rd
MSGFplus/man/msgfParFromID.Rd
MSGFplus/man/msgfParGUI.Rd
MSGFplus/man/msgfParInstrument-class.Rd
MSGFplus/man/msgfParIsotopeError-class.Rd
MSGFplus/man/msgfParLengthRange-class.Rd
MSGFplus/man/msgfParMatches-class.Rd
MSGFplus/man/msgfParModification-class.Rd
MSGFplus/man/msgfParModificationList-class.Rd
MSGFplus/man/msgfParNtt-class.Rd
MSGFplus/man/msgfParProtocol-class.Rd
MSGFplus/man/msgfParTda-class.Rd
MSGFplus/man/msgfParTolerance-class.Rd
MSGFplus/man/ntt.Rd
MSGFplus/man/protocol.Rd
MSGFplus/man/runMSGF.Rd
MSGFplus/man/tda.Rd
MSGFplus/man/tolerance.Rd
MSGFplus/tests
MSGFplus/tests/test-all.R
MSGFplus/tests/testthat
MSGFplus/tests/testthat/test_getMSGFpar.R
MSGFplus/tests/testthat/test_msgfParChargeRange.R
MSGFplus/tests/testthat/test_msgfParEnzyme.R
MSGFplus/tests/testthat/test_msgfParFragmentation.R
MSGFplus/tests/testthat/test_msgfParInstrument.R
MSGFplus/tests/testthat/test_msgfParIsotopeError.R
MSGFplus/tests/testthat/test_msgfParLengthRange.R
MSGFplus/tests/testthat/test_msgfParMatches.R
MSGFplus/tests/testthat/test_msgfParModification.R
MSGFplus/tests/testthat/test_msgfParModificationList.R
MSGFplus/tests/testthat/test_msgfParNtt.R
MSGFplus/tests/testthat/test_msgfParProtocol.R
MSGFplus/tests/testthat/test_msgfParTda.R
MSGFplus/tests/testthat/test_msgfParTolerance.R
MSGFplus/tests/testthat/test_setGet.R
MSGFplus/vignettes
MSGFplus/vignettes/Using_MSGFplus.Rmd
MSGFplus/vignettes/styles.css