MSGFplus (version 1.6.2)

tolerance: Get and set the parent tolerance in msgfPar objects

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
"tolerance"(object)
"toleranceRange"(object)
"toleranceUnit"(object)
"toleranceRange"(object) <- value
"toleranceUnit"(object) <- value
"tolerance"(object) <- value
"tolerance"(object) <- value

Arguments

object

An msgfPar object

value

For tolerance a character vector of length 2, each element of the form ' '. 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 ' '
• 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)