msgfParTolerance-class: A class handling parent ion tolerance

Description

This class defines a parent ion tolerance and provides methods to get correct system call parameters.

Usage

"show"(object)
"length"(x)
"getMSGFpar"(object)
msgfParTolerance(value, low, high, unit)

Arguments

object

An msgfParTolerance object

value

A numeric giving the upper and lower bounds of the tolerance

low

A numeric giving the lower bounds of the tolerance

high

A numeric giving the higher bounds of the tolerance

unit

The unit used. Either 'ppm' or 'Da'

Value

For length() An integer.For getMSGFpar() A string.For msgfParTolerance() An msgfParTolerance object.

Methods (by generic)

show: Short summary of msgfParTolerance object
length: Report the length of an msgfParTolerance object
getMSGFpar: Get system compliant function call

Slots

unit: The unit used to define the tolerance
low: The lower bound of the tolerance
high: The higher bound of the tolerance

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,msgfParProtocol-method, length,msgfParProtocol-method, msgfParProtocol, msgfParProtocol-class, show,msgfParProtocol-method; getMSGFpar,msgfParTda-method, length,msgfParTda-method, msgfParTda, msgfParTda-class, show,msgfParTda-method; msgfPar

Examples

Run this code

# Symmetric
tolerance <- msgfParTolerance(20, unit='ppm')

# Asymmetric
tolerance <- msgfParTolerance(low=0.5, high=1.5, unit='Da')

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