protocol: Get and set protocol in msgfPar objects

Description Usage Arguments Value Methods (by class) See Also Examples

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

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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

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parameters <- msgfPar(system.file(package='MSGFplus', 'extdata', 'milk-proteins.fasta'))
protocol(parameters) <- 'Phosphorylation'
protocol(parameters) <- 0
protocol(parameters)


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