matches: Get and set the number of matches in msgfPar objects

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

Description

These functions allow you to retrieve and set the number of matches per spectrum returned by MS-GF+

Usage

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matches(object)

matches(object) <- value

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

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

## S4 replacement method for signature 'msgfPar,msgfParMatches'
matches(object) <- value

Arguments

object

An msgfPar object

value

Either an integer or an msgfParMatches object

Value

In case of the getter an integer

Methods (by class)

  • msgfPar: Get the number of matches reported per spectrum

  • object = msgfPar,value = numeric: Set the number of matches reported per spectrum using an integer

  • object = msgfPar,value = msgfParMatches: Set the number of matches reported per spectrum using an msgfParMatches 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; 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'))
matches(parameters) <- 5
matches(parameters)


MSGFplus documentation built on May 20, 2017, 10:12 p.m.
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