MSGFplus: An interface between R and MS-GF+

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

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("MSGFplus")
AuthorThomas Lin Pedersen
Bioconductor views MassSpectrometry Proteomics
Date of publicationNone
MaintainerThomas Lin Pedersen <thomasp85@gmail.com>
LicenseGPL (>= 2)
Version1.10.0

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

Functions

chargeRange Man page
chargeRange<- Man page
chargeRange,msgfPar-method Man page
chargeRange<-,msgfPar,msgfParChargeRange-method Man page
chargeRange<-,msgfPar,numeric-method Man page
db Man page
db<- Man page
db<-,msgfPar,character-method Man page
db,msgfPar-method Man page
enzyme Man page
enzyme<- Man page
enzyme<-,msgfPar,character-method Man page
enzyme,msgfPar-method Man page
enzyme<-,msgfPar,msgfParEnzyme-method Man page
enzyme<-,msgfPar,numeric-method Man page
finished Man page
finished,msgfAsync-method Man page
fragmentation Man page
fragmentation<- Man page
fragmentation<-,msgfPar,character-method Man page
fragmentation,msgfPar-method Man page
fragmentation<-,msgfPar,msgfParFragmentation-method Man page
fragmentation<-,msgfPar,numeric-method Man page
getMSGFpar Man page
getMSGFpar,msgfParChargeRange-method Man page
getMSGFpar,msgfParEnzyme-method Man page
getMSGFpar,msgfParFragmentation-method Man page
getMSGFpar,msgfParInstrument-method Man page
getMSGFpar,msgfParIsotopeError-method Man page
getMSGFpar,msgfParLengthRange-method Man page
getMSGFpar,msgfParMatches-method Man page
getMSGFpar,msgfPar-method Man page
getMSGFpar,msgfParModificationList-method Man page
getMSGFpar,msgfParModification-method Man page
getMSGFpar,msgfParNtt-method Man page
getMSGFpar,msgfParProtocol-method Man page
getMSGFpar,msgfParTda-method Man page
getMSGFpar,msgfParTolerance-method Man page
import Man page
import,msgfAsync-method Man page
instrument Man page
instrument<- Man page
instrument<-,msgfPar,character-method Man page
instrument,msgfPar-method Man page
instrument<-,msgfPar,msgfParInstrument-method Man page
instrument<-,msgfPar,numeric-method Man page
isotopeError Man page
isotopeError<- Man page
isotopeError,msgfPar-method Man page
isotopeError<-,msgfPar,msgfParIsotopeError-method Man page
isotopeError<-,msgfPar,numeric-method Man page
length,msgfParChargeRange-method Man page
length,msgfParEnzyme-method Man page
length,msgfParFragmentation-method Man page
length,msgfParInstrument-method Man page
length,msgfParIsotopeError-method Man page
length,msgfParLengthRange-method Man page
length,msgfParMatches-method Man page
length,msgfPar-method Man page
length,msgfParModificationList-method Man page
length,msgfParNtt-method Man page
length,msgfParProtocol-method Man page
length,msgfParTda-method Man page
length,msgfParTolerance-method Man page
lengthRange Man page
lengthRange<- Man page
lengthRange,msgfPar-method Man page
lengthRange<-,msgfPar,msgfParLengthRange-method Man page
lengthRange<-,msgfPar,numeric-method Man page
matches Man page
matches<- Man page
matches,msgfPar-method Man page
matches<-,msgfPar,msgfParMatches-method Man page
matches<-,msgfPar,numeric-method Man page
mods Man page
mods<- Man page
mods,msgfPar-method Man page
mods<-,msgfPar,msgfParModificationList-method Man page
msgfAsync-class Man page
msgfPar Man page
msgfParChargeRange Man page
msgfParChargeRange-class Man page
msgfPar-class Man page
msgfParEnzyme Man page
msgfParEnzyme-class Man page
msgfParFragmentation Man page
msgfParFragmentation-class Man page
msgfParFromID Man page
msgfParGUI Man page
msgfParInstrument Man page
msgfParInstrument-class Man page
msgfParIsotopeError Man page
msgfParIsotopeError-class Man page
msgfParLengthRange Man page
msgfParLengthRange-class Man page
msgfParMatches Man page
msgfParMatches-class Man page
msgfParModification Man page
msgfParModification-class Man page
msgfParModificationList Man page
msgfParModificationList-class Man page
[[,msgfParModificationList,numeric,missing-method Man page
[[<-,msgfParModificationList,numeric,missing,msgfParModification Man page
msgfParNtt Man page
msgfParNtt-class Man page
msgfParProtocol Man page
msgfParProtocol-class Man page
msgfParTda Man page
msgfParTda-class Man page
msgfParTolerance Man page
msgfParTolerance-class Man page
MSGFplus-package Man page
nMod Man page
nMod<- Man page
nMod,msgfPar-method Man page
nMod<-,msgfPar,numeric-method Man page
ntt Man page
ntt<- Man page
ntt,msgfPar-method Man page
ntt<-,msgfPar,msgfParNtt-method Man page
ntt<-,msgfPar,numeric-method Man page
protocol Man page
protocol<- Man page
protocol<-,msgfPar,character-method Man page
protocol,msgfPar-method Man page
protocol<-,msgfPar,msgfParProtocol-method Man page
protocol<-,msgfPar,numeric-method Man page
runMSGF Man page
runMSGF,msgfPar-method Man page
running Man page
running,msgfAsync-method Man page
show,msgfParChargeRange-method Man page
show,msgfParEnzyme-method Man page
show,msgfParFragmentation-method Man page
show,msgfParInstrument-method Man page
show,msgfParIsotopeError-method Man page
show,msgfParLengthRange-method Man page
show,msgfParMatches-method Man page
show,msgfPar-method Man page
show,msgfParModificationList-method Man page
show,msgfParModification-method Man page
show,msgfParNtt-method Man page
show,msgfParProtocol-method Man page
show,msgfParTda-method Man page
show,msgfParTolerance-method Man page
tda Man page
tda<- Man page
tda<-,msgfPar,logical-method Man page
tda,msgfPar-method Man page
tda<-,msgfPar,msgfParTda-method Man page
tolerance Man page
tolerance<- Man page
tolerance<-,msgfPar,character-method Man page
tolerance,msgfPar-method Man page
tolerance<-,msgfPar,msgfParTolerance-method Man page
toleranceRange Man page
toleranceRange<- Man page
toleranceRange,msgfPar-method Man page
toleranceRange<-,msgfPar,numeric-method Man page
toleranceUnit Man page
toleranceUnit<- Man page
toleranceUnit<-,msgfPar,character-method Man page
toleranceUnit,msgfPar-method Man page

Files

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

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