RawDataParameters-class

The RawDataParameters class contains the slots for storing and accessing into a MS sample, and the essential parameters for performing its processing (deconvolution).

Automated compound deconvolution, alignment across samples, and identification of metabolites by spectral library matching in Gas Chromatography - Mass spectrometry (GC-MS) untargeted metabolomics. Outputs a table with compound names, matching scores and the integrated area of the compound for each sample. Package implementation is described in Domingo-Almenara et al. (2016) <doi:10.1021/acs.analchem.6b02927>.

Xavier Domingo-Almenara

erah

Automated Spectral Deconvolution, Alignment, and Metabolite
Identification in GC/MS-Based Untargeted Metabolomics

RawDataParameters-class function

<dl>
 <dt><code>data</code>:</dt>
<dd>The data matrix of the sample to be processed</dd> <dt><code>min.mz</code>:</dt>
<dd>The minimum adquired mz number</dd>	<dt><code>max.mz</code>:</dt>
<dd>The maximum adquired mz number</dd> <dt><code>start.time</code>:</dt>
<dd>Starting time of adquisition</dd> <dt><code>mz.resolution</code>:</dt>
<dd>Mz resolution</dd> <dt><code>scans.per.second</code>:</dt>
<dd>Scans per second</dd> <dt><code>avoid.processing.mz</code>:</dt>
<dd>Which mz do not have to be processed</dd> <dt><code>min.peak.width</code>:</dt>
<dd>Minimum peak width (stored in scans)</dd> <dt><code>min.peak.height</code>:</dt>
<dd>Minimum peak height</dd> <dt><code>noise.threshold</code>:</dt>
<dd>The noise threshold</dd> <dt><code>compression.coef</code>:</dt>
<dd>Compression coefficient (parameter for Orthogonal Signal Deconvolution)</dd> 
</dl>

Slots

Author

Class "RawDataParameters" — RawDataParameters-class

<dl>
 <dt><code>data</code>:</dt>
<dd>The data matrix of the sample to be processed</dd>

 <dt><code>min.mz</code>:</dt>
<dd>The minimum adquired mz number</dd>

	<dt><code>max.mz</code>:</dt>
<dd>The maximum adquired mz number</dd>

 <dt><code>start.time</code>:</dt>
<dd>Starting time of adquisition</dd>

 <dt><code>mz.resolution</code>:</dt>
<dd>Mz resolution</dd>

 <dt><code>scans.per.second</code>:</dt>
<dd>Scans per second</dd>

 <dt><code>avoid.processing.mz</code>:</dt>
<dd>Which mz do not have to be processed</dd>

 <dt><code>min.peak.width</code>:</dt>
<dd>Minimum peak width (stored in scans)</dd>

 <dt><code>min.peak.height</code>:</dt>
<dd>Minimum peak height</dd>

 <dt><code>noise.threshold</code>:</dt>
<dd>The noise threshold</dd>

 <dt><code>compression.coef</code>:</dt>
<dd>Compression coefficient (parameter for Orthogonal Signal Deconvolution)</dd>

 
</dl>

RawDataParameters-class: Class `"RawDataParameters"`

Description

Arguments

Slots

Author