A class handling modification characteristics

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Description

This class defines a single modification type that can be searched for by MS-GF+. Modifications are collected in a msgfParModificationList before adding them to msgfPar objects.

Usage

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

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

msgfParModification(name, composition = "", mass = as.numeric(NA), residues,
  type, position)

Arguments

object

An msgfParModification object

name

The name of the modification

composition

The molecular formular as a string for the modification. Loss of atoms are denoted with negative integers (e.g. O-1 for loss of oxygen)

mass

The monoisotopic mass change between a peptide without and with the given modification. Either composition or mass must be defined.

residues

The amino acids that the modification applies to. Given as their one-letter code in upper-case without any separation. Use '*' for all residues

type

Either 'fix' or 'opt' for fixed or optional

position

Where the modification can be. Either 'any', 'c-term', 'n-term', 'prot-c-term' or 'prot-n-term.

Value

For getMSGFpar() A string.

For msgfParModification() An msgfParModification object.

Methods (by generic)

  • getMSGFpar: Get system compliant function call

  • show: Short summary of msgfParModification object

Slots

composition

The molecular formula for the modification.

mass

The monoisotopic mass of the modification

residues

The amino acids the modification applies to

type

Whether the modification is optional or always present

position

The possibel position of the modification

name

The name of the modification

See Also

Other msgfParClasses: [[,msgfParModificationList,numeric,missing-method, [[<-,msgfParModificationList,numeric,missing,msgfParModification-method, getMSGFpar,msgfParModificationList-method, length,msgfParModificationList-method, msgfParModificationList, msgfParModificationList-class, show,msgfParModificationList-method; 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,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

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# Using composition
modification1 <- msgfParModification(
                                     name='Carbamidomethyl',
                                     composition='C2H3N1O1',
                                     residues='C',
                                     type='fix',
                                     position='any'
                                    )
# Using exact mass
modification2 <- msgfParModification(
                                     name='Oxidation',
                                     mass=15.994915,
                                     residues='M',
                                     type='opt',
                                     position='any'
                                    )

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