msgfParProtocol-class: A class handling protocol choice

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

Description

This class defines a protocol and provides methods to get correct system call parameters.

Usage

## S4 method for signature 'msgfParProtocol'
show(object)

## S4 method for signature 'msgfParProtocol'
length(x)

## S4 method for signature 'msgfParProtocol'
getMSGFpar(object)

msgfParProtocol(protocol)

Arguments

object	An msgfParProtocol object
x	An msgfParProtocol object
protocol	An integer or string specifying the protocol to use.

Value

For length() An integer.

For getMSGFpar() A string.

For msgfParProtocol() An msgfParProtocol object.

Methods (by generic)

• show: Short summary of msgfParProtocol object

• length: Report the length of an msgfParProtocol object

• getMSGFpar: Get system compliant function call

Slots

protocol

An integer specifying a specific protocol type

See Also

Other msgfParClasses: [[,msgfParModificationList,numeric,missing-method, [[<-,msgfParModificationList,numeric,missing,msgfParModification-method, getMSGFpar,msgfParModificationList-method, length,msgfParModificationList-method, msgfParModificationList, msgfParModificationList-class, show,msgfParModificationList-method; getMSGFpar,msgfPar-method, length,msgfPar-method, msgfPar-class, runMSGF,msgfPar-method, show,msgfPar-method; getMSGFpar,msgfParChargeRange-method, length,msgfParChargeRange-method, msgfParChargeRange, msgfParChargeRange-class, show,msgfParChargeRange-method; getMSGFpar,msgfParEnzyme-method, length,msgfParEnzyme-method, msgfParEnzyme, msgfParEnzyme-class, show,msgfParEnzyme-method; getMSGFpar,msgfParFragmentation-method, length,msgfParFragmentation-method, msgfParFragmentation, msgfParFragmentation-class, show,msgfParFragmentation-method; getMSGFpar,msgfParInstrument-method, length,msgfParInstrument-method, msgfParInstrument, msgfParInstrument-class, show,msgfParInstrument-method; getMSGFpar,msgfParIsotopeError-method, length,msgfParIsotopeError-method, msgfParIsotopeError, msgfParIsotopeError-class, show,msgfParIsotopeError-method; getMSGFpar,msgfParLengthRange-method, length,msgfParLengthRange-method, msgfParLengthRange, msgfParLengthRange-class, show,msgfParLengthRange-method; getMSGFpar,msgfParMatches-method, length,msgfParMatches-method, msgfParMatches, msgfParMatches-class, show,msgfParMatches-method; getMSGFpar,msgfParModification-method, msgfParModification, msgfParModification-class, show,msgfParModification-method; getMSGFpar,msgfParNtt-method, length,msgfParNtt-method, msgfParNtt, msgfParNtt-class, show,msgfParNtt-method; getMSGFpar,msgfParTda-method, length,msgfParTda-method, msgfParTda, msgfParTda-class, show,msgfParTda-method; getMSGFpar,msgfParTolerance-method, length,msgfParTolerance-method, msgfParTolerance, msgfParTolerance-class, show,msgfParTolerance-method; msgfPar

Examples

protocol <- msgfParProtocol(0)
protocol <- msgfParProtocol('No protocol')

thomasp85/MSGFplus-release documentation built on May 31, 2019, 11:09 a.m.