msgfParTolerance-class: A class handling parent ion tolerance

Description Usage Arguments Value Methods (by generic) Slots See Also Examples

Description

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

Usage

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

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

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

msgfParTolerance(value, low, high, unit)

Arguments

object

An msgfParTolerance object

x

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

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,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

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

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


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