tolerance: Get and set the parent tolerance in msgfPar objects

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

Description

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

Usage

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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)

See Also

Other msgfPar-getter_setter: chargeRange, db, enzyme, fragmentation, instrument, isotopeError, lengthRange, matches, mods, ntt, protocol, tda

Examples

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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)

MSGFplus documentation built on Nov. 17, 2017, 9:04 a.m.