tolerance: Get and set the parent tolerance in msgfPar objects

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

Description

These functions allow you to retrieve and set the tolerance used for matching parent ions to peptides in the database

Usage

tolerance(object)

tolerance(object) <- value

toleranceRange(object)

toleranceRange(object) <- value

toleranceUnit(object)

toleranceUnit(object) <- value

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

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

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

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

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

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

## S4 replacement method for signature 'msgfPar,msgfParTolerance'
tolerance(object) <- value

Arguments

object	An msgfPar object
value	For tolerance a character vector of length 2, each element of the form '<value> <unit>'. For toleranceUnit a string. For toleranceRange a numeric vector of length 2.

Value

For tolerance a character vector with the lower and upper tolerance limit with unit. For toleranceUnit a string with the unit used. For toleranceRange a numeric vector with lower and upper tolerance limit.

Methods (by class)

• msgfPar: Get the lower and upper bounds of the tolerance

• msgfPar: Get the lower and upper bounds of the tolerance

• msgfPar: Get the unit the tolerance is measured in

• object = msgfPar,value = numeric: Set the lower and upper bounds of the tolerance using a numeric vector of length 2

• object = msgfPar,value = character: Set the unit the tolerance is meassured in

• object = msgfPar,value = character: Set the lower and upper bounds of the tolerance using a character vector of length 2, where each element is of the form '<value> <unit>'

• object = msgfPar,value = msgfParTolerance: Set the lower and upper bounds of the tolerance using an msgfParTolerance 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; 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

Examples

parameters <- msgfPar(system.file(package='MSGFplus', 'extdata', 'milk-proteins.fasta'))
tolerance(parameters) <- c('20 ppm', '20 ppm')
toleranceUnit(parameters) <- 'Da'
toleranceRange(parameters) <- c(1.5, 1.5)
tolerance(parameters)

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