ntt: Get and set cleavage specificity in msgfPar objects

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

Get and set cleavage specificity in msgfPar objects

Description

These functions allow you to retrieve and set the quality of cleavage allowed during search in MS-GF+ (number of tolerable termini - ntt)

Usage

ntt(object)

ntt(object) <- value

## S4 method for signature 'msgfPar'
ntt(object)

## S4 replacement method for signature 'msgfPar,numeric'
ntt(object) <- value

## S4 replacement method for signature 'msgfPar,msgfParNtt'
ntt(object) <- value

Arguments

object	An msgfPar object
value	An integer or an msgfParNtt object

Value

In case of the getter an integer between 0 and 2

Methods (by class)

• msgfPar: Get the number of tolerable termini

• object = msgfPar,value = numeric: Set the ntt using an integer

• object = msgfPar,value = msgfParNtt: Set the ntt using an msgfParNtt object

See Also

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

Examples

parameters <- msgfPar(system.file(package='MSGFplus', 'extdata', 'milk-proteins.fasta'))
ntt(parameters) <- 2
ntt(parameters)

thomasp85/MSGFplus documentation built on Oct. 2, 2024, 9:26 a.m.