plotProfile

plotProfile,MetaboSet-method

Plots the chromatophic profiles of the compounds found by eRah.

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

plotProfile function

<dl><dt>Experiment</dt>
<dd>A 'MetaboSet' S4 object containing the experiment after being deconolved, aligned and (optionally) identified.</dd>
<dt>AlignId</dt>
<dd>the Id identificator for the compound to be shown.</dd>
<dt>per.class</dt>
<dd>logical. if TRUE (by default) the profiles are shown one color per class, if FALSE one color per sample.</dd>
<dt>xlim</dt>
<dd>x axsis (retention time) limits (see <code><a href="/link/plot.default?package=erah&version=2.0.1" data-mini-rdoc="erah::plot.default">plot.default</a></code>).</dd>
<dt>cols</dt>
<dd>vector of colors. Colors are used cyclically.</dd></dl>

Arguments

Xavier Domingo-Almenara. xavier.domingo@urv.cat

Author

Plotting chromatographic profile — plotProfile

<dl>

<dt>Experiment</dt>
<dd>A 'MetaboSet' S4 object containing the experiment after being deconolved, aligned and (optionally) identified.</dd>


<dt>AlignId</dt>
<dd>the Id identificator for the compound to be shown.</dd>


<dt>per.class</dt>
<dd>logical. if TRUE (by default) the profiles are shown one color per class, if FALSE one color per sample.</dd>


<dt>xlim</dt>
<dd>x axsis (retention time) limits (see <code><a href='https://rdrr.io/r/graphics/plot.default.html'>plot.default</a></code>).</dd>


<dt>cols</dt>
<dd>vector of colors. Colors are used cyclically.</dd>

</dl>

plotProfile: Plotting chromatographic profile

Description

Usage

Arguments

Author

See Also