fragmentation: Get and set fragmentation in msgfPar objects

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

Description

These functions allow you to retrieve and set the fragmentation method used during acquisition

Usage

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fragmentation(object)

fragmentation(object) <- value

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

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

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

## S4 replacement method for signature 'msgfPar,msgfParFragmentation'
fragmentation(object) <- value

Arguments

object

An msgfPar object

value

Either an integer, string or msgfParFragmentation object

Value

In case of the getter a named integer

Methods (by class)

  • msgfPar: Get the fragmentation method currently used

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

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

  • object = msgfPar,value = msgfParFragmentation: Set the fragmentation method using an msgfParFragmentation 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; 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; 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

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parameters <- msgfPar(system.file(package='MSGFplus', 'extdata', 'milk-proteins.fasta'))
fragmentation(parameters) <- 'CID'
fragmentation(parameters) <- 3
fragmentation(parameters)


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