enzyme: Get and set enzyme in msgfPar objects

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

Get and set enzyme in msgfPar objects

Description

These functions allow you to retrieve and set the enzyme used for digestion during sample treatment.

Usage

enzyme(object)

enzyme(object) <- value

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

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

## S4 replacement method for signature 'msgfPar,character'
enzyme(object) <- value

## S4 replacement method for signature 'msgfPar,msgfParEnzyme'
enzyme(object) <- value

Arguments

object	An msgfPar object
value	Either an integer, string or msgfParEnzyme object

Value

In case of the getter a named integer

Methods (by class)

• msgfPar: Get the enzyme currently used

• object = msgfPar,value = numeric: Set the enzyme to use using the key for the enzyme

• object = msgfPar,value = character: Set the enzyme to use using the name of the enzyme

• object = msgfPar,value = msgfParEnzyme: Set the enzyme to use using an msgfParEnzyme object

See Also

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

Examples

parameters <- msgfPar(system.file(package='MSGFplus', 'extdata', 'milk-proteins.fasta'))
enzyme(parameters) <- 'Trypsin'
enzyme(parameters) <- 3
enzyme(parameters)

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