tda: Get and set use of target-decoy approach in msgfPar objects

In thomasp85/MSGFplus: An interface between R and MS-GF+

Description

These functions allow you to retrieve and set whether the target-decoy approach should be used to estimate q-values.

Usage

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

Arguments

object	An msgfPar object
value	Either a boolean or msgfParTda object

Value

In case of the getter a boolean indicating whether tda is used or not

Methods (by class)

• 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

See Also

Other msgfPar-getter_setter: chargeRange, db, enzyme, fragmentation, instrument, isotopeError, lengthRange, matches, mods, ntt, protocol, tolerance

Examples

parameters <- msgfPar(system.file(package='MSGFplus', 'extdata', 'milk-proteins.fasta'))
tda(parameters) <- TRUE
tda(parameters)

thomasp85/MSGFplus documentation built on Aug. 29, 2020, 5:23 a.m.