protocol: Get and set protocol in msgfPar objects

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

Description

These functions allow you to retrieve and set the protocol used during MS-GF+ analysis. This allows you to fine tune the analysis in case of labelled or phosphoproteomic analysis

Usage

protocol(object)

protocol(object) <- value

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

## S4 replacement method for signature 'msgfPar,numeric'
protocol(object) <- value

## S4 replacement method for signature 'msgfPar,character'
protocol(object) <- value

## S4 replacement method for signature 'msgfPar,msgfParProtocol'
protocol(object) <- value

Arguments

object	An msgfPar object
value	Either an integer, a string or an msgfParProtocol object

Value

In case of the getter a named integer

Methods (by class)

• msgfPar: Get the protocol currently used

• object = msgfPar,value = numeric: Set the protocol using the key for the protocol

• object = msgfPar,value = character: Set the protocol using the name of the protocol

• object = msgfPar,value = msgfParProtocol: Set the protocol using an msgfParProtocol object

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; mods, mods,msgfPar-method, mods<-, mods<-,msgfPar,msgfParModificationList-method, nMod, nMod,msgfPar-method, nMod<-, nMod<-,msgfPar,numeric-method; ntt, ntt,msgfPar-method, ntt<-, ntt<-,msgfPar,msgfParNtt-method, ntt<-,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'))
protocol(parameters) <- 'Phosphorylation'
protocol(parameters) <- 0
protocol(parameters)

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