msgfParEnzyme-class: A class handling enzyme selection

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

Description

This class defines a digestion enzyme selection and provides methods to get correct system call parameters.

Usage

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

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

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

msgfParEnzyme(enzyme)

Arguments

object	An msgfParEnzyme object
x	An msgfParEnzyme object
enzyme	Either an integer or a string

Value

For length() An integer.

For getMSGFpar() A string.

For msgfParEnzyme() An msgfParEnzyme object.

Methods (by generic)

• show: Short summary of msgfParEnzyme object

• length: Report the length of an msgfParEnzyme object

• getMSGFpar: Get system compliant function call

Slots

enzyme

An integer specifiying the selection of enzyme. See the detail section of msgfPar

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,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,msgfParProtocol-method, length,msgfParProtocol-method, msgfParProtocol, msgfParProtocol-class, show,msgfParProtocol-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

enzyme <- msgfParEnzyme(1)
enzyme <- msgfParEnzyme('Trypsin')

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