tolerance: Get and set the parent tolerance in msgfPar objects

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

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

## 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)

thomasp85/MSGFplus documentation built on Oct. 2, 2024, 9:26 a.m.