msgfParModificationList-class: A class handling a list of modifications

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

Description

This class defines a set of modifications and a maximum number of modifications allowed per peptide.

Usage

## S4 method for signature 'msgfParModificationList'
show(object)

## S4 method for signature 'msgfParModificationList'
length(x)

## S4 method for signature 'msgfParModificationList'
getMSGFpar(object)

## S4 method for signature 'msgfParModificationList,numeric,missing'
x[[i, j, ...]]

## S4 replacement method for signature 
## 'msgfParModificationList,numeric,missing,msgfParModification'
x[[i,
  j, ...]] <- value

msgfParModificationList(nMod, modifications = list())

Arguments

object	An msgfParModificationList object
x	An msgfParModificationList object
i	The index of the modification
j	Ignored
...	Ignored
value	An msgfParModification object
nMod	The maximum allowed number of modifications to expect on any peptide
modifications	A list of msgfParModification objects

Value

For length() An integer.

For getMSGFpar() A string.

For '[[' A msgfParModification object

For msgfParModificationList() An msgfParModificationList object.

Methods (by generic)

• show: Short summary of msgfParModificationList object

• length: Report the length of an msgfParModificationList object

• getMSGFpar: Get system compliant function call

• [[: Get the i'th modification

• [[<-: Set or change the i'th modification

Slots

nMod

The maximum allowed number of modifications to expect on any peptide

modifications

A list of msgfParModification objects

See Also

Other msgfParClasses: getMSGFpar,msgfPar-method, length,msgfPar-method, msgfPar-class, runMSGF,msgfPar-method, show,msgfPar-method; getMSGFpar,msgfParChargeRange-method, length,msgfParChargeRange-method, msgfParChargeRange, msgfParChargeRange-class, show,msgfParChargeRange-method; getMSGFpar,msgfParEnzyme-method, length,msgfParEnzyme-method, msgfParEnzyme, msgfParEnzyme-class, show,msgfParEnzyme-method; getMSGFpar,msgfParFragmentation-method, length,msgfParFragmentation-method, msgfParFragmentation, msgfParFragmentation-class, show,msgfParFragmentation-method; getMSGFpar,msgfParInstrument-method, length,msgfParInstrument-method, msgfParInstrument, msgfParInstrument-class, show,msgfParInstrument-method; getMSGFpar,msgfParIsotopeError-method, length,msgfParIsotopeError-method, msgfParIsotopeError, msgfParIsotopeError-class, show,msgfParIsotopeError-method; getMSGFpar,msgfParLengthRange-method, length,msgfParLengthRange-method, msgfParLengthRange, msgfParLengthRange-class, show,msgfParLengthRange-method; getMSGFpar,msgfParMatches-method, length,msgfParMatches-method, msgfParMatches, msgfParMatches-class, show,msgfParMatches-method; getMSGFpar,msgfParModification-method, msgfParModification, msgfParModification-class, show,msgfParModification-method; getMSGFpar,msgfParNtt-method, length,msgfParNtt-method, msgfParNtt, msgfParNtt-class, show,msgfParNtt-method; getMSGFpar,msgfParProtocol-method, length,msgfParProtocol-method, msgfParProtocol, msgfParProtocol-class, show,msgfParProtocol-method; getMSGFpar,msgfParTda-method, length,msgfParTda-method, msgfParTda, msgfParTda-class, show,msgfParTda-method; getMSGFpar,msgfParTolerance-method, length,msgfParTolerance-method, msgfParTolerance, msgfParTolerance-class, show,msgfParTolerance-method; msgfPar

Examples

modification1 <- msgfParModification(
                                     name='Carbamidomethyl',
                                     composition='C2H3N1O1',
                                     residues='C',
                                     type='fix',
                                     position='any'
                                    )
modification2 <- msgfParModification(
                                     name='Oxidation',
                                     mass=15.994915,
                                     residues='M',
                                     type='opt',
                                     position='any'
                                    )
modificationlist <- msgfParModificationList(
                                            nMod=2,
                                            modifications=list(
                                                modification1,
                                                modification2
                                            )
                                           )
modificationlist[[3]] <- msgfParModification(
                                             name='Gln->pyro-Glu',
                                             composition='H-3N-1',
                                             residues='Q',
                                             type='opt',
                                             position='N-term'
                                            )

thomasp85/MSGFplus-release documentation built on May 31, 2019, 11:09 a.m.