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yufree committed Feb 2, 2023
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Package: metabobook
Title: Metabolomics Workflow
Version: 2023.1
Imports: survival (>= 2.40-1),bookdown,multtest,xcms,faahKO,qvalue,CAMERA,sva,limma,RColorBrewer,AER,DiagrammeR,rentrez,reshape,ggplot2
Imports: bookdown,sva,limma,RColorBrewer,AER,DiagrammeR,rentrez,reshape,ggplot2
2 changes: 1 addition & 1 deletion _output.yml
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Expand Up @@ -8,5 +8,5 @@ bookdown::gitbook:
<li><a href="https://github.com/yufree/metaworkflow" target="blank">Published with bookdown</a></li>
edit:
link: https://github.com/yufree/metaworkflow/edit/master/%s
download: ["pub"]
download: ["epub"]
bookdown::epub_book: default
72 changes: 36 additions & 36 deletions docs/annotation.html
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Expand Up @@ -439,22 +439,22 @@ <h2><span class="header-section-number">7.4</span> Molecular Formula Assignment<
<ul>
<li>Apply heuristic restrictions for number of elements during formula generation. This is the table for known compounds:</li>
</ul>
<pre><code>## Mass.Range.[Da] Library C.max H.max N.max O.max P.max S.max F.max Cl.max
## 1 &lt; 500 DNP 29 72 10 18 4 7 15 8
## 2 &lt;NA&gt; Wiley 39 72 20 20 9 10 16 10
## 3 &lt; 1000 DNP 66 126 25 27 6 8 16 11
## 4 &lt;NA&gt; Wiley 78 126 20 27 9 14 34 12
## 5 &lt; 2000 DNP 115 236 32 63 6 8 16 11
## 6 &lt;NA&gt; Wiley 156 180 20 40 9 14 48 12
## 7 &lt; 3000 DNP 162 208 48 78 6 9 16 11
## Br.max Si.max
## 1 5 NA
## 2 4 8
## 3 8 NA
## 4 8 14
## 5 8 NA
## 6 10 15
## 7 8 NA</code></pre>
<pre><code>## Mass.Range.[Da] Library C.max H.max N.max O.max P.max S.max
## 1 &lt; 500 DNP 29 72 10 18 4 7
## 2 &lt;NA&gt; Wiley 39 72 20 20 9 10
## 3 &lt; 1000 DNP 66 126 25 27 6 8
## 4 &lt;NA&gt; Wiley 78 126 20 27 9 14
## 5 &lt; 2000 DNP 115 236 32 63 6 8
## 6 &lt;NA&gt; Wiley 156 180 20 40 9 14
## 7 &lt; 3000 DNP 162 208 48 78 6 9
## F.max Cl.max Br.max Si.max
## 1 15 8 5 NA
## 2 16 10 4 8
## 3 16 11 8 NA
## 4 34 12 8 14
## 5 16 11 8 NA
## 6 48 12 10 15
## 7 16 11 8 NA</code></pre>
<ul>
<li><p>Perform LEWIS and SENIOR check. The LEWIS rule demands that molecules consisting of main group elements, especially carbon, nitrogen and oxygen, share electrons in a way that all atoms have completely filled s, p-valence shells (‘<a href="https://en.wikipedia.org/wiki/Octet_rule">octet rule</a>’). Senior’s theorem requires three essential conditions for the existence of molecular graphs</p>
<ul>
Expand All @@ -466,26 +466,26 @@ <h2><span class="header-section-number">7.4</span> Molecular Formula Assignment<
<li><p>Perform H/C ratio check (hydrogen/carbon ratio). In most cases the hydrogen/carbon ratio does not exceed H/C &gt; 3 with rare exception such as in methylhydrazine (CH6N2). Conversely, the H/C ratio is usually smaller than 2, and should not be less than 0.125 like in the case of tetracyanopyrrole (C8HN5).</p></li>
<li><p>Perform NOPS ratio check (N, O, P, S/C ratios).</p></li>
</ul>
<pre><code>## Element.ratios Common.range.(covering.99.7%) Extended.range.(covering.99.99%)
## 1 H/C 0.2–3.1 0.1–6
## 2 F/C 0–1.5 0–6
## 3 Cl/C 0–0.8 0–2
## 4 Br/C 0–0.8 0–2
## 5 N/C 0–1.3 0–4
## 6 O/C 0–1.2 0–3
## 7 P/C 0–0.3 0–2
## 8 S/C 0–0.8 0–3
## 9 Si/C 0–0.5 0–1
## Extreme.range.(beyond.99.99%)
## 1 &lt; 0.1 and 6–9
## 2 &gt; 1.5
## 3 &gt; 0.8
## 4 &gt; 0.8
## 5 &gt; 1.3
## 6 &gt; 1.2
## 7 &gt; 0.3
## 8 &gt; 0.8
## 9 &gt; 0.5</code></pre>
<pre><code>## Element.ratios Common.range.(covering.99.7%)
## 1 H/C 0.2–3.1
## 2 F/C 0–1.5
## 3 Cl/C 0–0.8
## 4 Br/C 0–0.8
## 5 N/C 0–1.3
## 6 O/C 0–1.2
## 7 P/C 0–0.3
## 8 S/C 0–0.8
## 9 Si/C 0–0.5
## Extended.range.(covering.99.99%) Extreme.range.(beyond.99.99%)
## 1 0.1–6 &lt; 0.1 and 6–9
## 2 0–6 &gt; 1.5
## 3 0–2 &gt; 0.8
## 4 0–2 &gt; 0.8
## 5 0–4 &gt; 1.3
## 6 0–3 &gt; 1.2
## 7 0–2 &gt; 0.3
## 8 0–3 &gt; 0.8
## 9 0–1 &gt; 0.5</code></pre>
<ul>
<li>Perform heuristic HNOPS probability check (H, N, O, P, S/C high probability ratios)</li>
</ul>
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4 changes: 2 additions & 2 deletions docs/introduction.html
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Expand Up @@ -523,8 +523,8 @@ <h2><span class="header-section-number">1.3</span> Trends in Metabolomics<a href
</div>
<div id="workflow-1" class="section level2 hasAnchor" number="1.4">
<h2><span class="header-section-number">1.4</span> Workflow<a href="introduction.html#workflow-1" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<div id="htmlwidget-beabc24ff1a59a8c19f6" style="width:300px;height:480px;" class="grViz html-widget "></div>
<script type="application/json" data-for="htmlwidget-beabc24ff1a59a8c19f6">{"x":{"diagram":"digraph workflow {\nnode [shape = box]\nA [label = \"raw data\"]\nB [label = \"open source format\"]\nC [label = \"DoE folder\"]\nD [label = \"peaks list\"]\nE [label = \"retention time correction\"]\nF [label = \"peaks grouping\"]\nG [label = \"peaks filling\"]\nH [label = \"raw peaks\"]\nI [label = \"data visulization\"]\nJ [label = \"batch effects correction\"]\nK [label = \"corrected peaks\"]\nL [label = \"annotation\"]\nM [label = \"metabolomics pathway analysis\"]\nN [label = \"omics analysis\"]\nO [label = \"biomarkers discovery/diagnoise\"]\n\nA -> B -> C -> D -> E -> F -> G -> H\nH -> I\nI -> J\nH -> J -> K -> L\nL -> M -> N\nL -> O\n }","config":{"engine":"dot","options":null}},"evals":[],"jsHooks":[]}</script>
<div id="htmlwidget-e36ce9489c4bd308ea22" style="width:300px;height:480px;" class="grViz html-widget "></div>
<script type="application/json" data-for="htmlwidget-e36ce9489c4bd308ea22">{"x":{"diagram":"digraph workflow {\nnode [shape = box]\nA [label = \"raw data\"]\nB [label = \"open source format\"]\nC [label = \"DoE folder\"]\nD [label = \"peaks list\"]\nE [label = \"retention time correction\"]\nF [label = \"peaks grouping\"]\nG [label = \"peaks filling\"]\nH [label = \"raw peaks\"]\nI [label = \"data visulization\"]\nJ [label = \"batch effects correction\"]\nK [label = \"corrected peaks\"]\nL [label = \"annotation\"]\nM [label = \"metabolomics pathway analysis\"]\nN [label = \"omics analysis\"]\nO [label = \"biomarkers discovery/diagnoise\"]\n\nA -> B -> C -> D -> E -> F -> G -> H\nH -> I\nI -> J\nH -> J -> K -> L\nL -> M -> N\nL -> O\n }","config":{"engine":"dot","options":null}},"evals":[],"jsHooks":[]}</script>

</div>
</div>
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2 changes: 1 addition & 1 deletion docs/search_index.json
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4 changes: 2 additions & 2 deletions docs/workflow-2.html
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Expand Up @@ -406,8 +406,8 @@ <h1><span class="header-section-number">Chapter 5</span> Workflow<a href="workfl
<span id="cb7-13"><a href="workflow-2.html#cb7-13" aria-hidden="true" tabindex="-1"></a><span class="st">B --&gt; E</span></span>
<span id="cb7-14"><a href="workflow-2.html#cb7-14" aria-hidden="true" tabindex="-1"></a><span class="st">C --&gt; H</span></span>
<span id="cb7-15"><a href="workflow-2.html#cb7-15" aria-hidden="true" tabindex="-1"></a><span class="st">&quot;</span>)</span></code></pre></div>
<div class="DiagrammeR html-widget html-fill-item-overflow-hidden html-fill-item" id="htmlwidget-f971d9607432eaa28cb3" style="width:672px;height:480px;"></div>
<script type="application/json" data-for="htmlwidget-f971d9607432eaa28cb3">{"x":{"diagram":"\nflowchart TB\nI(peak-picking) --> C\nC(visulization) --> D(normalization/batch correction)\nD --> A(annotation/identification)\nA --> H(statistical analysis)\nC --> A --> B(omics analysis)\nD --> H\nB --> H\nH --> E(experimental validation)\nA --> E\nH --> A\nB --> E\nC --> H\n"},"evals":[],"jsHooks":[]}</script>
<div class="DiagrammeR html-widget html-fill-item-overflow-hidden html-fill-item" id="htmlwidget-dc0f64dbf7ed44db7581" style="width:672px;height:480px;"></div>
<script type="application/json" data-for="htmlwidget-dc0f64dbf7ed44db7581">{"x":{"diagram":"\nflowchart TB\nI(peak-picking) --> C\nC(visulization) --> D(normalization/batch correction)\nD --> A(annotation/identification)\nA --> H(statistical analysis)\nC --> A --> B(omics analysis)\nD --> H\nB --> H\nH --> E(experimental validation)\nA --> E\nH --> A\nB --> E\nC --> H\n"},"evals":[],"jsHooks":[]}</script>
<div id="platform-for-metabolomics-data-analysis" class="section level2 hasAnchor" number="5.1">
<h2><span class="header-section-number">5.1</span> Platform for metabolomics data analysis<a href="workflow-2.html#platform-for-metabolomics-data-analysis" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p>Here is a list for related open source <a href="http://strimmerlab.org/notes/mass-spectrometry.html">projects</a></p>
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