protocol {MSGFplus} | R Documentation |
These functions allow you to retrieve and set the protocol used during MS-GF+ analysis. This allows you to fine tune the analysis in case of labelled or phosphoproteomic analysis
protocol(object) protocol(object) <- value ## S4 method for signature 'msgfPar' protocol(object) ## S4 replacement method for signature 'msgfPar,numeric' protocol(object) <- value ## S4 replacement method for signature 'msgfPar,character' protocol(object) <- value ## S4 replacement method for signature 'msgfPar,msgfParProtocol' protocol(object) <- value
object |
An msgfPar object |
value |
Either an integer, a string or an msgfParProtocol object |
In case of the getter a named integer
msgfPar
: Get the protocol currently used
object = msgfPar,value = numeric
: Set the protocol using the key for the protocol
object = msgfPar,value = character
: Set the protocol using the name of the protocol
object = msgfPar,value = msgfParProtocol
: Set the protocol using an msgfParProtocol object
Other msgfPar-getter_setter: chargeRange
,
db
, enzyme
,
fragmentation
, instrument
,
isotopeError
, lengthRange
,
matches
, mods
,
ntt
, tda
,
tolerance
parameters <- msgfPar(system.file(package='MSGFplus', 'extdata', 'milk-proteins.fasta')) protocol(parameters) <- 'Phosphorylation' protocol(parameters) <- 0 protocol(parameters)