getSample.rtmsSpectrum

getSampleFromSpectrum

Extracts a sample object of class <code>rtmsSample</code> from a single spectrum object
of class <code>rtmsSample</code> usin g a list of peaks

Quickly imports, processes, analyzes, and visualizes mass-spectrometric
data.  Includes functions for easily extracting specific data and measurements
from large (multi-gigabyte) raw Bruker data files, as well as a set of S3 object
classes for manipulating and measuring mass spectrometric peaks and plotting
peaks and spectra using the 'ggplot2' package.

Nathaniel Twarog

rtms

R Toolkit for Mass Spectrometry

Mary Ashley Rimmer

getSample.rtmsSpectrum function

<dl><dt>x</dt>
<dd>The spectrum object</dd>
<dt>peaks</dt>
<dd>A list of peak objects of class <code>rtmsPeak</code></dd>
<dt>...</dt>
<dd>Additional parameters</dd>
<dt>spectrum</dt>
<dd>A full spectrum of class <code>rtmsSpectrum</code></dd>
<dt>freqSpacing</dt>
<dd>If TRUE (the default), local maxima (estimated via
quadratic interpolation) are calculated in inverse m/z (or frequency) space,
as in FTMS spectra. If FALSE, maxima are calculated directy in m/z space</dd>
<dt>threshold</dt>
<dd>If NULL, all local maxima will be returned for each
subsample; if set to particular value, only those maxima above that threshold
will be returned.</dd></dl>

Arguments

<ul>
<li><code>getSample(rtmsSpectrum)</code>: The S3 method <code>getSample</code> for objects
of class <code>rtmsSpectrum</code>; calls <code>getSampleFromSpectrum</code></li>
</ul>

Functions

Extract a sample from an RTMS spectrum object — getSample.rtmsSpectrum

<dl>

<dt>x</dt>
<dd>The spectrum object</dd>


<dt>peaks</dt>
<dd>A list of peak objects of class <code>rtmsPeak</code></dd>


<dt>...</dt>
<dd>Additional parameters</dd>


<dt>spectrum</dt>
<dd>A full spectrum of class <code>rtmsSpectrum</code></dd>


<dt>freqSpacing</dt>
<dd>If TRUE (the default), local maxima (estimated via
quadratic interpolation) are calculated in inverse m/z (or frequency) space,
as in FTMS spectra. If FALSE, maxima are calculated directy in m/z space</dd>


<dt>threshold</dt>
<dd>If NULL, all local maxima will be returned for each
subsample; if set to particular value, only those maxima above that threshold
will be returned.</dd>

</dl>

getSample.rtmsSpectrum: Extract a sample from an RTMS spectrum object

Description

Usage

Value

Arguments

Functions

Examples