MSGFplus (version 1.6.2)

mods: Get and set the modifications in msgfPar objects

Description

These functions allow you to retrieve and set the specific modifications allowed on peptides during MS-GF+ search, as well as the number allowed on each peptide

Usage

mods(object)
mods(object) <- value
nMod(object)
nMod(object) <- value
"mods"(object)
"mods"(object) <- value
"nMod"(object)
"nMod"(object) <- value

Arguments

object

An msgfPar object

value

An msgfParModificationList object or in the case of nMod an integer

Value

For the getter an msgfParModificationList object or an integer (in the case of nMod)

Methods (by class)

• msgfPar: Get the list of modifications allowed during peptide search
• object = msgfPar,value = msgfParModificationList: Set the list of modifications allowed during peptide search
• msgfPar: Get the number of peptides allowed per peptide during search
• object = msgfPar,value = numeric: Set the number of peptides allowed per peptide during search using an integer

See Also

Other msgfPar-getter_setter: chargeRange, chargeRange,msgfPar-method, chargeRange<-, chargeRange<-,msgfPar,msgfParChargeRange-method, chargeRange<-,msgfPar,numeric-method; db, db,msgfPar-method, db<-, db<-,msgfPar,character-method; enzyme, enzyme,msgfPar-method, enzyme<-, enzyme<-,msgfPar,character-method, enzyme<-,msgfPar,msgfParEnzyme-method, enzyme<-,msgfPar,numeric-method; fragmentation, fragmentation,msgfPar-method, fragmentation<-, fragmentation<-,msgfPar,character-method, fragmentation<-,msgfPar,msgfParFragmentation-method, fragmentation<-,msgfPar,numeric-method; instrument, instrument,msgfPar-method, instrument<-, instrument<-,msgfPar,character-method, instrument<-,msgfPar,msgfParInstrument-method, instrument<-,msgfPar,numeric-method; isotopeError, isotopeError,msgfPar-method, isotopeError<-, isotopeError<-,msgfPar,msgfParIsotopeError-method, isotopeError<-,msgfPar,numeric-method; lengthRange, lengthRange,msgfPar-method, lengthRange<-, lengthRange<-,msgfPar,msgfParLengthRange-method, lengthRange<-,msgfPar,numeric-method; matches, matches,msgfPar-method, matches<-, matches<-,msgfPar,msgfParMatches-method, matches<-,msgfPar,numeric-method; ntt, ntt,msgfPar-method, ntt<-, ntt<-,msgfPar,msgfParNtt-method, ntt<-,msgfPar,numeric-method; protocol, protocol,msgfPar-method, protocol<-, protocol<-,msgfPar,character-method, protocol<-,msgfPar,msgfParProtocol-method, protocol<-,msgfPar,numeric-method; tda, tda,msgfPar-method, tda<-, tda<-,msgfPar,logical-method, tda<-,msgfPar,msgfParTda-method; tolerance, tolerance,msgfPar-method, tolerance<-, tolerance<-,msgfPar,character-method, tolerance<-,msgfPar,msgfParTolerance-method, toleranceRange, toleranceRange,msgfPar-method, toleranceRange<-, toleranceRange<-,msgfPar,numeric-method, toleranceUnit, toleranceUnit,msgfPar-method, toleranceUnit<-, toleranceUnit<-,msgfPar,character-method

Examples

parameters <- msgfPar(system.file(package='MSGFplus', 'extdata', 'milk-proteins.fasta'))
nMod(parameters) <- 2
mods(parameters)[[1]] <- msgfParModification(
                                                      name='Carbamidomethyl',
                                                      composition='C2H3N1O1',
                                                      residues='C',
                                                      type='fix',
                                                      position='any'
                                                     )
mods(parameters)