msgfParModificationList-class {MSGFplus} | R Documentation |
This class defines a set of modifications and a maximum number of modifications allowed per peptide.
## 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())
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 |
For length() An integer.
For getMSGFpar() A string.
For '[[' A msgfParModification object
For msgfParModificationList() An msgfParModificationList object.
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
nMod
The maximum allowed number of modifications to expect on any peptide
modifications
A list of msgfParModification
objects
Other msgfParClasses: msgfPar-class
,
msgfParChargeRange-class
,
msgfParEnzyme-class
,
msgfParFragmentation-class
,
msgfParInstrument-class
,
msgfParIsotopeError-class
,
msgfParLengthRange-class
,
msgfParMatches-class
,
msgfParModification-class
,
msgfParNtt-class
,
msgfParProtocol-class
,
msgfParTda-class
,
msgfParTolerance-class
,
msgfPar
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' )