protocol: Get and set protocol in msgfPar objects

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

Description

These functions allow you to retrieve and set the protocol used during MS-GF+ analysis. This allows you to fine tune the analysis in case of labelled or phosphoproteomic analysis

Usage

protocol(object)

protocol(object) <- value

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

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

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

## S4 replacement method for signature 'msgfPar,msgfParProtocol'
protocol(object) <- value

Arguments

object	An msgfPar object
value	Either an integer, a string or an msgfParProtocol object

Value

In case of the getter a named integer

Methods (by class)

• msgfPar: Get the protocol currently used

• object = msgfPar,value = numeric: Set the protocol using the key for the protocol

• object = msgfPar,value = character: Set the protocol using the name of the protocol

• object = msgfPar,value = msgfParProtocol: Set the protocol using an msgfParProtocol object

See Also

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

Examples

parameters <- msgfPar(system.file(package='MSGFplus', 'extdata', 'milk-proteins.fasta'))
protocol(parameters) <- 'Phosphorylation'
protocol(parameters) <- 0
protocol(parameters)

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