msgfParTolerance-class: A class handling parent ion tolerance

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

Description

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

Usage

## 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

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

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

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