Commit 9bc6a616 authored by Jakob Wirbel's avatar Jakob Wirbel Committed by GitHub

Merge pull request #3 from jakob-wirbel/master

Include Matomo tracking for the SIAMCAT website
parents 83a10225 60d61b9d
......@@ -16,7 +16,18 @@
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......@@ -151,7 +162,7 @@ siamcat.fr &lt;-<span class="st"> </span><span class="kw"><a href="../reference/
<pre><code>## + Keeping labels of 141 sample(s).</code></pre>
<pre><code>## +++ checking sample number per class</code></pre>
<pre><code>## +++ checking overlap between samples and metadata</code></pre>
<pre><code>## + finished validate.data in 0.041 s</code></pre>
<pre><code>## + finished validate.data in 0.039 s</code></pre>
<p>We can load the data from the Chinese study in a similar way and also create a <code>SIAMCAT</code> object for the holdout dataset.</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># features</span>
feat.cn &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/read.table">read.table</a></span>(fn.feat.cn, <span class="dt">sep=</span><span class="st">'</span><span class="ch">\t</span><span class="st">'</span>, <span class="dt">quote=</span><span class="st">""</span>,
......@@ -176,7 +187,7 @@ siamcat.cn &lt;-<span class="st"> </span><span class="kw"><a href="../reference/
<pre><code>## + Keeping labels of 128 sample(s).</code></pre>
<pre><code>## +++ checking sample number per class</code></pre>
<pre><code>## +++ checking overlap between samples and metadata</code></pre>
<pre><code>## + finished validate.data in 0.032 s</code></pre>
<pre><code>## + finished validate.data in 0.031 s</code></pre>
</div>
<div id="model-building-on-the-french-dataset" class="section level1">
<h1 class="hasAnchor">
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......@@ -412,7 +423,7 @@ feat &lt;-<span class="st"> </span>meta.and.features<span class="op">$</span>fea
## cancer
## Label used as control:
## healthy</code></pre>
<pre><code>## + finished create.label.from.metadata in 0.015 s</code></pre>
<pre><code>## + finished create.label.from.metadata in 0.016 s</code></pre>
</div>
<div id="metagenomeseq-format-files" class="section level2">
<h2 class="hasAnchor">
......@@ -464,7 +475,7 @@ siamcat &lt;-<span class="st"> </span><span class="kw"><a href="../reference/sia
<pre><code>## Data set has only 8 training examples of class Case .
## Note that a dataset this small/skewed is not necessarily suitable for analysis in this pipeline.</code></pre>
<pre><code>## +++ checking overlap between samples and metadata</code></pre>
<pre><code>## + finished validate.data in 0.439 s</code></pre>
<pre><code>## + finished validate.data in 0.433 s</code></pre>
</div>
</div>
<div id="creating-a-siamcat-class-object" class="section level1">
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......@@ -152,7 +163,7 @@
## CRC
## Label used as control:
## CTR</code></pre>
<pre><code>## + finished create.label.from.metadata in 0.002 s</code></pre>
<pre><code>## + finished create.label.from.metadata in 0.001 s</code></pre>
<p>Now we have all the ingredients to create a <code>SIAMCAT</code> object. Please have a look at the <a href="SIAMCAT_read-in.html">vignette about input formats</a> for more information about supported formats and other ways to create a <code>SIAMCAT</code> object.</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">siamcat &lt;-<span class="st"> </span><span class="kw"><a href="../reference/siamcat.html">siamcat</a></span>(<span class="dt">feat=</span>feat.crc.zeller,
<span class="dt">label=</span>label.crc.zeller,
......@@ -162,7 +173,7 @@
<pre><code>## + Keeping labels of 141 sample(s).</code></pre>
<pre><code>## +++ checking sample number per class</code></pre>
<pre><code>## +++ checking overlap between samples and metadata</code></pre>
<pre><code>## + finished validate.data in 0.058 s</code></pre>
<pre><code>## + finished validate.data in 0.057 s</code></pre>
<p>A few information about the <code>siamcat</code> object can be accessed with the <code>show</code> function from <code>phyloseq</code> (<code>SIAMCAT</code> builds on the <code>phyloseq</code> data structure):</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">show</span>(siamcat)</code></pre></div>
<pre><code>## siamcat-class object
......@@ -247,13 +258,13 @@ models[[<span class="dv">1</span>]]</code></pre></div>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">siamcat &lt;-<span class="st"> </span><span class="kw"><a href="../reference/make.predictions.html">make.predictions</a></span>(siamcat)
pred_matrix &lt;-<span class="st"> </span><span class="kw"><a href="../reference/pred_matrix-methods.html">pred_matrix</a></span>(siamcat)</code></pre></div>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/head">head</a></span>(pred_matrix)</code></pre></div>
<pre><code>## CV_rep1 CV_rep2
## CCIS27304052ST-3-0 0.19880497 0.09535739
## CCIS15794887ST-4-0 0.25670422 0.16473066
## CCIS74726977ST-3-0 0.59187395 0.63774235
## CCIS16561622ST-4-0 0.54217795 0.09439314
## CCIS79210440ST-3-0 0.28578571 0.23673264
## CCIS82507866ST-3-0 0.08502265 0.07268986</code></pre>
<pre><code>## CV_rep1 CV_rep2
## CCIS27304052ST-3-0 0.05627524 0.1227390
## CCIS15794887ST-4-0 0.06400252 0.0941945
## CCIS74726977ST-3-0 0.41996493 0.2777645
## CCIS16561622ST-4-0 0.34675575 0.2208130
## CCIS79210440ST-3-0 0.44411220 0.1147398
## CCIS82507866ST-3-0 0.07560513 0.0656949</code></pre>
</div>
</div>
<div id="model-evaluation-and-interpretation" class="section level1">
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......@@ -214,6 +225,13 @@ eLife, (<strong>2019</strong>) 8:e42693</p>
<p>See Figure 3 - figure supplement 1</p>
</blockquote>
</li>
<li>
<p><strong><a href="https://www.nature.com/articles/s41591-019-0406-6">Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer</a></strong><br><em>Wirbel J, Pyl PT, Kartal E, Zych K, Kashani A, Milanese A, Fleck JS, Voigt AY, Palleja A, Ponnudurai R, Sunagawa S, Coelho LP, Schrotz-King P, Vogtmann E, Habermann N, Niméus E, Thomas AM, Manghi P, Gandini S, Serrano D, Mizutani S, Shiroma H, Shiba S, Shibata T, Yachida S, Yamada T, Waldron L, Naccarati A, Segata N, Sinha R, Ulrich CM, Brenner H, Arumugam M, Bork P, Zeller G</em><br>
Nature Medicine, (<strong>2019</strong>) [Epub ahead of print]</p>
<blockquote>
<p>In this publication, <code>SIAMCAT</code> is used extensively for holdout testing</p>
</blockquote>
</li>
</ul>
<p>If you used <code>SIAMCAT</code> in your publication, <a href="mailto:zeller@embl.de">let us know</a>!</p>
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Communities And host phenoTypes — SIAMCAT-package • SIAMCAT</title>
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<meta property="og:title" content="Assign a new list containing a cross-validation split to a
SIAMCAT object — data_split&lt;-" />
......@@ -42,16 +28,22 @@ SIAMCAT object" />
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