plotChr

plotChr,MetaboSet-method

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

plotChr function

<dl><dt>Experiment</dt>
<dd>A 'MetaboSet' S4 object containing the experiment.</dd>
<dt>N.sample</dt>
<dd>Integer. The number of the sample to query.</dd>
<dt>type</dt>
<dd>The type of plotting, Base Ion Chromatogram (BIC), Total Ion Chromatogram (TIC), or Extracted Ion Chromatogram (EIC).</dd>
<dt>xlim</dt>
<dd>The range in minutes, separated by comas: c(rt.min, rt.max) of the limits of plotting. By default, all the chromatogram is plotted.</dd>
<dt>mz</dt>
<dd>Just when EIC is selected. The range separated by comas: c(mz.min, mz.max) or a vector of numbers: c(50,67,80), of the masses to be ploted.</dd></dl>

Arguments

Plotting sample chromatogram — plotChr

<dl>

<dt>Experiment</dt>
<dd>A 'MetaboSet' S4 object containing the experiment.</dd>


<dt>N.sample</dt>
<dd>Integer. The number of the sample to query.</dd>


<dt>type</dt>
<dd>The type of plotting, Base Ion Chromatogram (BIC), Total Ion Chromatogram (TIC), or Extracted Ion Chromatogram (EIC).</dd>


<dt>xlim</dt>
<dd>The range in minutes, separated by comas: c(rt.min, rt.max) of the limits of plotting. By default, all the chromatogram is plotted.</dd>


<dt>mz</dt>
<dd>Just when EIC is selected. The range separated by comas: c(mz.min, mz.max) or a vector of numbers: c(50,67,80), of the masses to be ploted.</dd>

</dl>

plotChr: Plotting sample chromatogram

Description

Usage

Arguments

See Also