mods: Get and set the modifications in msgfPar objects

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

Description

These functions allow you to retrieve and set the specific modifications allowed on peptides during MS-GF+ search, as well as the number allowed on each peptide

Usage

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mods(object)

mods(object) <- value

nMod(object)

nMod(object) <- value

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

## S4 replacement method for signature 'msgfPar,msgfParModificationList'
mods(object) <- value

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

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

Arguments

object

An msgfPar object

value

An msgfParModificationList object or in the case of nMod an integer

Value

For the getter an msgfParModificationList object or an integer (in the case of nMod)

Methods (by class)

See Also

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

Examples

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parameters <- msgfPar(system.file(package='MSGFplus', 'extdata', 'milk-proteins.fasta'))
nMod(parameters) <- 2
mods(parameters)[[1]] <- msgfParModification(
                                                      name='Carbamidomethyl',
                                                      composition='C2H3N1O1',
                                                      residues='C',
                                                      type='fix',
                                                      position='any'
                                                     )
mods(parameters)

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