automatic site/doc update [skip ci]

docs/examples/report.html

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docs/handbook_bd/404.html

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docs/handbook_bd/FCCalc.html

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@@ -364,14 +364,14 @@ <h2><span class="header-section-number">8.10</span> Fold changes<a href="FCCalc.
 #&gt; $PVTestFunc
 #&gt; function (x, y) 
 #&gt; t.test(x, y, paired = TRUE)$p.value
-#&gt; &lt;bytecode: 0x5637f8281008&gt;
-#&gt; &lt;environment: 0x5637f82816d0&gt;
+#&gt; &lt;bytecode: 0x560030853fc8&gt;
+#&gt; &lt;environment: 0x560030850898&gt;
 #&gt; 
 #&gt; $PVAdjFunc
 #&gt; function (pv) 
 #&gt; p.adjust(pv, &quot;BH&quot;)
-#&gt; &lt;bytecode: 0x5637f8281318&gt;
-#&gt; &lt;environment: 0x5637f82816d0&gt;</code></pre>
+#&gt; &lt;bytecode: 0x5600308542d8&gt;
+#&gt; &lt;environment: 0x560030850898&gt;</code></pre>
 <p>In this example we generate a <code>list</code> with parameters in order to make a comparison between two replicate groups: <code>before</code> and <code>after</code>. Several advanced parameters are available to tweak the calculation process. These are explained in the reference manual (<code>?featureGroups</code>).</p>
 <p>The <code>as.data.table</code> function for feature groups is used to perform the FC calculations.</p>
 <div class="sourceCode" id="cb267"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb267-1"><a href="FCCalc.html#cb267-1" aria-hidden="true" tabindex="-1"></a>myFCParams <span class="ot">&lt;-</span> <span class="fu">getFCParams</span>(<span class="fu">c</span>(<span class="st">&quot;solvent-pos&quot;</span>, <span class="st">&quot;standard-pos&quot;</span>)) <span class="co"># compare solvent/standard</span></span>

docs/handbook_bd/MSLibraries.html

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docs/handbook_bd/TPs.html

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@@ -345,8 +345,8 @@ <h1>
 <h1><span class="header-section-number">7</span> Transformation product screening<a href="TPs.html#TPs" class="anchor-section" aria-label="Anchor link to header"></a></h1>
 <p>This chapter describes the various functionality for screening of <em>transformation products</em> (TPs), which are introduced since <code>patRoon</code> 2.0. Screening for TPs, i.e. chemicals that are formed from a <em>parent</em> chemical by e.g. chemical or biological processes, has broad applications. For this reason, the TP screening related functionality is designed to be flexible, thus allowing one to use a workflow that is best suited for a particular study.</p>
 <p>Regardless, the TP screening workflow in <code>patRoon</code> can be roughly summarized as follows:</p>
-<div id="htmlwidget-749849d59477ade7b65a" style="width:500px;height:90px;" class="grViz html-widget"></div>
-<script type="application/json" data-for="htmlwidget-749849d59477ade7b65a">{"x":{"diagram":"\ndigraph Workflow {\n  graph [ rankdir = LR ]\n  node [ shape = box,\n         fixedsize = true,\n         width = 2.2,\n         height = 1,\n         fontsize = 18,\n         fillcolor = darkseagreen1,\n         style = filled ]\n\n    \"Parent screening\" -> \"Obtaining TPs\" -> \"TP screening\" -> \"Linking parent/TPs\"\n}","config":{"engine":"dot","options":null}},"evals":[],"jsHooks":[]}</script>
+<div id="htmlwidget-a6e7a69e5554b5899f6a" style="width:500px;height:90px;" class="grViz html-widget"></div>
+<script type="application/json" data-for="htmlwidget-a6e7a69e5554b5899f6a">{"x":{"diagram":"\ndigraph Workflow {\n  graph [ rankdir = LR ]\n  node [ shape = box,\n         fixedsize = true,\n         width = 2.2,\n         height = 1,\n         fontsize = 18,\n         fillcolor = darkseagreen1,\n         style = filled ]\n\n    \"Parent screening\" -> \"Obtaining TPs\" -> \"TP screening\" -> \"Linking parent/TPs\"\n}","config":{"engine":"dot","options":null}},"evals":[],"jsHooks":[]}</script>
 <ul>
 <li><strong>Parent screening</strong> During this step a common <code>patRoon</code> workflow is used to screen for the parent chemicals of interest. This could be a full non-target analysis with compound annotation or a relative simple suspect or target screening.</li>
 <li><strong>Obtaining TPs</strong> Data is obtained of potential TPs for the parents of interest. The TPs may originate from a library or predicted <em>in-silico</em>. Note that in some workflows this step is omitted (discussed later).</li>

docs/handbook_bd/TPsExamples.html

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docs/handbook_bd/adducts.html

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docs/handbook_bd/advanced.html

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@@ -371,8 +371,8 @@ <h3><span class="header-section-number">6.5.1</span> Initiating a sets workflow
 <span id="cb159-8"><a href="advanced.html#cb159-8" aria-hidden="true" tabindex="-1"></a>fGroups <span class="ot">&lt;-</span> <span class="fu">makeSet</span>(fGroupsPos, fGroupsNeg, <span class="at">groupAlgo =</span> <span class="st">&quot;openms&quot;</span>,</span>
 <span id="cb159-9"><a href="advanced.html#cb159-9" aria-hidden="true" tabindex="-1"></a>                   <span class="at">adducts =</span> <span class="fu">c</span>(<span class="st">&quot;[M+H]+&quot;</span>, <span class="st">&quot;[M-H]-&quot;</span>))</span></code></pre></div>
 <p>Visually, this workflow looks like this:</p>
-<div id="htmlwidget-5a1cf2015ec3a319a05c" style="width:250px;height:300px;" class="grViz html-widget"></div>
-<script type="application/json" data-for="htmlwidget-5a1cf2015ec3a319a05c">{"x":{"diagram":"\ndigraph Workflow {\n  graph [ rankdir = TB, compound = true ]\n  node [ shape = box,\n         fixedsize = true,\n         width = 2.2,\n         height = 0.6,\n         fontsize = 16,\n         fillcolor = darkseagreen1,\n         style = filled ]\n\n    \"Find features (+)\" -> \"Group features (+)\" -> \"filter (+)\" -> \"makeSet\"\n    \"Find features (-)\" -> \"Group features (-)\" -> \"filter (-)\" -> \"makeSet\"\n    \"makeSet\" -> \"...\"\n}","config":{"engine":"dot","options":null}},"evals":[],"jsHooks":[]}</script>
+<div id="htmlwidget-4a999f37357fef26d116" style="width:250px;height:300px;" class="grViz html-widget"></div>
+<script type="application/json" data-for="htmlwidget-4a999f37357fef26d116">{"x":{"diagram":"\ndigraph Workflow {\n  graph [ rankdir = TB, compound = true ]\n  node [ shape = box,\n         fixedsize = true,\n         width = 2.2,\n         height = 0.6,\n         fontsize = 16,\n         fillcolor = darkseagreen1,\n         style = filled ]\n\n    \"Find features (+)\" -> \"Group features (+)\" -> \"filter (+)\" -> \"makeSet\"\n    \"Find features (-)\" -> \"Group features (-)\" -> \"filter (-)\" -> \"makeSet\"\n    \"makeSet\" -> \"...\"\n}","config":{"engine":"dot","options":null}},"evals":[],"jsHooks":[]}</script>
 <p>Of course, any other processing steps on the feature groups data such as subsetting and <a href="intReview.html#intReview">visually checking features</a> are also possible before the sets workflow is initiated. Furthermore, it is also possible to perform <a href="incorpAdductIso.html#incorpAdductIso">adduct annotations</a> prior to grouping, which is an alternative way to improve neutralization to what <a href="setsAdducts.html#setsAdducts">was discussed before</a>.</p>
 </div>
 <div id="inspecting-and-converting-set-objects" class="section level3 hasAnchor" number="6.5.2">

docs/handbook_bd/advanced_usage.html

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docs/handbook_bd/annotation.html

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@@ -344,8 +344,8 @@ <h1>
 <div id="annotation" class="section level2 hasAnchor" number="4.6">
 <h2><span class="header-section-number">4.6</span> Annotation<a href="annotation.html#annotation" class="anchor-section" aria-label="Anchor link to header"></a></h2>
 <p>The annotation consists of collecting MS peak lists and then formula and/or compound annotation:</p>
-<div id="htmlwidget-7ba7721ad896f5c08144" style="width:500px;height:120px;" class="grViz html-widget"></div>
-<script type="application/json" data-for="htmlwidget-7ba7721ad896f5c08144">{"x":{"diagram":"\ndigraph Annotation {\n  graph [ rankdir = LR ]\n  node [ shape = box,\n         fixedsize = true,\n         width = 2.3,\n         height = 1,\n         fontsize = 18,\n         fillcolor = darkseagreen1,\n         style = filled ]\n\n    \"MS peak lists\" -> \"Formula annotation\"\n    \"MS peak lists\" -> \"Compound annotation\"\n    \"Formula annotation\":n -> \"Suspect annotation\":n [style = dotted]\n    \"Compound annotation\":s -> \"Suspect annotation\":s [style = dotted]\n    \"Formula annotation\":e -> \"Compound annotation\":e [style = dotted, constraint = false]\n}","config":{"engine":"dot","options":null}},"evals":[],"jsHooks":[]}</script>
+<div id="htmlwidget-fba5ea725559922426cc" style="width:500px;height:120px;" class="grViz html-widget"></div>
+<script type="application/json" data-for="htmlwidget-fba5ea725559922426cc">{"x":{"diagram":"\ndigraph Annotation {\n  graph [ rankdir = LR ]\n  node [ shape = box,\n         fixedsize = true,\n         width = 2.3,\n         height = 1,\n         fontsize = 18,\n         fillcolor = darkseagreen1,\n         style = filled ]\n\n    \"MS peak lists\" -> \"Formula annotation\"\n    \"MS peak lists\" -> \"Compound annotation\"\n    \"Formula annotation\":n -> \"Suspect annotation\":n [style = dotted]\n    \"Compound annotation\":s -> \"Suspect annotation\":s [style = dotted]\n    \"Formula annotation\":e -> \"Compound annotation\":e [style = dotted, constraint = false]\n}","config":{"engine":"dot","options":null}},"evals":[],"jsHooks":[]}</script>
 <p>Note that compound annotation is normally not dependent upon formula annotation. However, formula data can be used to improve ranking of candidates afterwards by the <code>addFormulaScoring()</code> function, which will be discussed later in this section. Furthermore, suspect annotation is not mandatory, and may use data from peak lists, formulae and/or comounds.</p>
 <div id="ms-peak-lists" class="section level3 hasAnchor" number="4.6.1">
 <h3><span class="header-section-number">4.6.1</span> MS peak lists<a href="annotation.html#ms-peak-lists" class="anchor-section" aria-label="Anchor link to header"></a></h3>

docs/handbook_bd/automatic-installation-windows-only.html

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docs/handbook_bd/basic-quantitative-and-regression-analysis.html

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docs/handbook_bd/caching.html

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docs/handbook_bd/compclust.html

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