mods: Get and set the modifications in msgfPar objects

In thomasp85/MSGFplus-release: An interface between R and MS-GF+

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

## S4 method for signature 'msgfPar'
mods(object)

## S4 replacement method for signature 'msgfPar,msgfParModificationList'
mods(object) <- value

## S4 method for signature 'msgfPar'
nMod(object)

## S4 replacement method for signature 'msgfPar,numeric'
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)

thomasp85/MSGFplus-release documentation built on May 31, 2019, 11:09 a.m.