fragmentation: Get and set fragmentation in msgfPar objects

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

Get and set fragmentation in msgfPar objects

Description

These functions allow you to retrieve and set the fragmentation method used during acquisition

Usage

fragmentation(object)

fragmentation(object) <- value

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

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

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

## S4 replacement method for signature 'msgfPar,msgfParFragmentation'
fragmentation(object) <- value

Arguments

object	An msgfPar object
value	Either an integer, string or msgfParFragmentation object

Value

In case of the getter a named integer

Methods (by class)

• msgfPar: Get the fragmentation method currently used

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

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

• object = msgfPar,value = msgfParFragmentation: Set the fragmentation method using an msgfParFragmentation object

See Also

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

Examples

parameters <- msgfPar(system.file(package='MSGFplus', 'extdata', 'milk-proteins.fasta'))
fragmentation(parameters) <- 'CID'
fragmentation(parameters) <- 3
fragmentation(parameters)

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