mods {MSGFplus} | R Documentation |
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
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
object |
An msgfPar object |
value |
An msgfParModificationList object or in the case of nMod an integer |
For the getter an msgfParModificationList object or an integer (in the case of nMod)
msgfPar
: Get the list of modifications allowed during
peptide search
object = msgfPar,value = msgfParModificationList
: Set the list of modifications allowed during
peptide search
msgfPar
: Get the number of peptides allowed per peptide
during search
object = msgfPar,value = numeric
: Set the number of peptides allowed per peptide
during search using an integer
Other msgfPar-getter_setter: chargeRange
,
db
, enzyme
,
fragmentation
, instrument
,
isotopeError
, lengthRange
,
matches
, ntt
,
protocol
, tda
,
tolerance
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)