MSGFplus: ntt – R documentation

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ntt

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

Examples

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

MSGFplus

An interface between R and MS-GF+

v1.24.0

GPL (>= 2)

Authors

Thomas Lin Pedersen

Initial release

2020-09-01

ntt