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vignettes/clr/BioNovoGene/BioDeep/Chemistry/MetaLib/RefMet.html
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<!DOCTYPE html> | ||
<html> | ||
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<head> | ||
<title>BioNovoGene.BioDeep.Chemistry.MetaLib.RefMet</title> | ||
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> | ||
<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes" /> | ||
<link rel="stylesheet" type="text/css" href="https://mzkit.org/assets/js/page.css"> | ||
</head> | ||
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<body> | ||
<div class="container"> | ||
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<table style="width: 100%;"> | ||
<tr> | ||
<td>RefMet {BioNovoGene.BioDeep.Chemistry.MetaLib}</td> | ||
<td style="text-align: right;">.NET clr documentation</td> | ||
</tr> | ||
</table> | ||
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<h2>RefMet</h2> | ||
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<h3>Description</h3> | ||
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<p>RefMet: A Reference set of Metabolite names</p> | ||
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<p>RefMet Naming Conventions | ||
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The names used in RefMet are generally based on common, officially accepted terms and | ||
incorporate notations which are appropriate for the type of analytical technique used. | ||
In general, high-throughput untargeted MS experiments are not capable of deducing | ||
stereochemistry, double bond position/geometry and sn position (for glycerolipids/ | ||
lycerophospholipids). Secondly, the type of MS technique employed, as well as the mass | ||
accuacy of the instrument will produce identifications at different levels of detail. | ||
For example, MS/MS methods are capable of identifying acyl chain substituents in lipids | ||
(e.g. PC 16:0/20:4) whereas MS methods only using precursor ion information might report | ||
these ions as "sum-composition" species (e.g. PC 36:4). RefMet covers both types of | ||
notations in an effort to enable data-sharing and comparative analysis of metabolomics | ||
data, using an analytical chemistry-centric approach. | ||
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The "sum-composition" lipid species indicate the number Of carbons And number Of "double | ||
bond equivalents" (DBE), but Not chain positions Or Double bond regiochemistry And geometry. | ||
The concept Of a Double bond equivalent unites a range Of chemical functionality which | ||
gives rise To isobaric features by mass spectometry. For example a chain containing a ring | ||
results In loss Of 2 hydrogen atoms (compared To a linear Structure) And thus has 1 DBE | ||
since the mass And molecular formula Is identical To a linear Structure With one Double bond. | ||
Similarly, conversion Of a hydroxyl group To ketone results In loss Of 2 hydrogen atoms, | ||
therefore the ketone Is assigned 1 DBE. Where applicable, the number Of oxygen atoms Is added | ||
To the abbreviation, separated by a semi-colon. Oxygen atoms In the Class-specific functional | ||
group (e.g. the carboxylic acid group For fatty acids Or the phospholcholine group For PC) | ||
are excluded. In the Case Of sphingolipids, all oxygen atoms apart from the amide oxygen are | ||
included, In order To discrminate, For example, between 1-deoxyceramides (;O), ceramides (;O2) | ||
And phytoceramides (;O3). | ||
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Some notes pertaining To different metabolite classes are outlined below.</p> | ||
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<h3>Declare</h3> | ||
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<pre> | ||
<code id="clr_ts"> | ||
# namespace BioNovoGene.BioDeep.Chemistry.MetaLib | ||
export class RefMet { | ||
exactmass: string; | ||
formula: string; | ||
inchi_key: string; | ||
main_class: string; | ||
pubchem_cid: string; | ||
refmet_name: string; | ||
smiles: string; | ||
sub_class: string; | ||
super_class: string; | ||
} | ||
</code> | ||
</pre> | ||
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<h3>.NET clr type reference tree</h3> | ||
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this clr type has no other .net clr type reference. | ||
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<hr /> | ||
<div style="text-align: center;">[Package <em>{$package}</em> version {$version} <a | ||
href="../{$package}.html">Index</a>] | ||
</div> | ||
</div> | ||
</body> | ||
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<script type="text/javascript" src="https://mzkit.org/assets/js/R_syntax.js"></script> | ||
<script type="text/javascript" src="https://mzkit.org/assets/js/highlights.js"></script> | ||
<script type="text/javascript">r_highlights("clr_ts");</script> | ||
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</html> |
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<!DOCTYPE html> | ||
<html> | ||
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<head> | ||
<title>singleCell_labels</title> | ||
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> | ||
<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes" /> | ||
<link rel="stylesheet" type="text/css" href="https://mzkit.org/assets/js/page.css"> | ||
</head> | ||
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<body> | ||
<div class="container"> | ||
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<table style="width: 100%;"> | ||
<tr> | ||
<td>singleCell_labels {SingleCells}</td> | ||
<td style="text-align: right;">R Documentation</td> | ||
</tr> | ||
</table> | ||
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<h2>singleCell_labels</h2> | ||
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<h3>Description</h3> | ||
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singleCell_labels | ||
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<h3>Usage</h3> | ||
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<div style="width: 100%; padding-left: 3%; color: black;"> | ||
<pre><code class='language-R' style="color: black; font-weight:normal;"><strong>singleCell_labels</strong>(<i>x</i>);</code></pre> | ||
</div> | ||
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<h3>Arguments</h3> | ||
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<table> | ||
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</table> | ||
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<h3 style="display: none;">Details</h3> | ||
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<h3 style="display: block">Authors</h3> | ||
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BioNovoGene | ||
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<h3>Value</h3> | ||
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this function returns data object of type string.<h4>clr value class</h4><ul><li>string</li></ul> | ||
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<h3 style="display: none;">Examples</h3> | ||
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<hr /> | ||
<div style="text-align: center;">[Package <em>SingleCells</em> version 1.0.0.0 <a | ||
href="../SingleCells.html">Index</a>] | ||
</div> | ||
</div> | ||
</body> | ||
|
||
<script type="text/javascript" src="https://mzkit.org/assets/js/R_syntax.js"></script> | ||
<script type="text/javascript" src="https://mzkit.org/assets/js/highlights.js"></script> | ||
<script type="text/javascript">r_highlights("example_r");</script> | ||
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</html> |
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<!DOCTYPE html> | ||
<html> | ||
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<head> | ||
<title>do matrix data normalization via total peak sum</title> | ||
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> | ||
<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes" /> | ||
<link rel="stylesheet" type="text/css" href="https://mzkit.org/assets/js/page.css"> | ||
</head> | ||
|
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<body> | ||
<div class="container"> | ||
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<table style="width: 100%;"> | ||
<tr> | ||
<td>total_peaksum {SingleCells}</td> | ||
<td style="text-align: right;">R Documentation</td> | ||
</tr> | ||
</table> | ||
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<h2>do matrix data normalization via total peak sum</h2> | ||
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<h3>Description</h3> | ||
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<h3>Usage</h3> | ||
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<div style="width: 100%; padding-left: 3%; color: black;"> | ||
<pre><code class='language-R' style="color: black; font-weight:normal;"><strong>total_peaksum</strong>(<i>x</i>, | ||
<i>scale</i> = <span style='color: green;'>1000000</span>);</code></pre> | ||
</div> | ||
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<h3>Arguments</h3> | ||
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<table> | ||
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<dt>x</dt> | ||
<dd><p>[as <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/SingleCells/Deconvolute/MzMatrix.html">MzMatrix</a>]</p></dd> | ||
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<dt>scale</dt> | ||
<dd><p>[as double]</p></dd> | ||
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</table> | ||
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<h3 style="display: none;">Details</h3> | ||
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<h3 style="display: block">Authors</h3> | ||
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BioNovoGene | ||
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<h3>Value</h3> | ||
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this function returns data object of type <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/SingleCells/Deconvolute/MzMatrix.html">MzMatrix</a>.<h4>clr value class</h4><ul><li><a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/SingleCells/Deconvolute/MzMatrix.html">MzMatrix</a></li></ul> | ||
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<h3 style="display: none;">Examples</h3> | ||
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<hr /> | ||
<div style="text-align: center;">[Package <em>SingleCells</em> version 1.0.0.0 <a | ||
href="../SingleCells.html">Index</a>] | ||
</div> | ||
</div> | ||
</body> | ||
|
||
<script type="text/javascript" src="https://mzkit.org/assets/js/R_syntax.js"></script> | ||
<script type="text/javascript" src="https://mzkit.org/assets/js/highlights.js"></script> | ||
<script type="text/javascript">r_highlights("example_r");</script> | ||
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</html> |
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