Get and set use of target-decoy approach in msgfPar objects
These functions allow you to retrieve and set whether the target-decoy approach should be used to estimate q-values.
tda(object) tda(object) <- value ## S4 method for signature 'msgfPar' tda(object) ## S4 replacement method for signature 'msgfPar,logical' tda(object) <- value ## S4 replacement method for signature 'msgfPar,msgfParTda' tda(object) <- value
object |
An msgfPar object |
value |
Either a boolean or msgfParTda object |
In case of the getter a boolean indicating whether tda is used or not
msgfPar: Get whether tda is currently used for FDR estimation
object = msgfPar,value = logical: Set the use of tda using a boolean (TRUE/FALSE)
object = msgfPar,value = msgfParTda: Set the use of tda using an msgfParTda object
Other msgfPar-getter_setter: chargeRange,
db, enzyme,
fragmentation, instrument,
isotopeError, lengthRange,
matches, mods,
ntt, protocol,
tolerance
parameters <- msgfPar(system.file(package='MSGFplus', 'extdata', 'milk-proteins.fasta')) tda(parameters) <- TRUE tda(parameters)
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