MSGFplus: An interface between R and MS-GF+

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

AuthorThomas Lin Pedersen
Date of publicationNone
MaintainerThomas Lin Pedersen <thomasp85@gmail.com>
LicenseGPL (>= 2)
Version1.8.0

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

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