tolerance: Get and set the parent tolerance in msgfPar objects

In MSGFplus: 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, db, enzyme, fragmentation, instrument, isotopeError, lengthRange, matches, mods, ntt, protocol, tda

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)

MSGFplus documentation built on Nov. 8, 2020, 6:48 p.m.