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<!DOCTYPE html>
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<meta name="generator" content="pandoc">
<meta name="author" content="Aleksandra Dąbrowska" />
<meta name="author" content="Alicja Gosiewska" />
<title>MLExpResso – NGS, Metylacja, Expresja, R i sporo kawy</title>
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<div class="reveal">
<div class="slides">
<section>
<h1 class="title">MLExpResso – NGS, Metylacja, Expresja, R i sporo kawy</h1>
<h2 class="author">Aleksandra Dąbrowska</h2>
<h2 class="author">Alicja Gosiewska</h2>
<h3 class="date">29.09.2017</h3>
</section>
<section><section id="grupa-mi2-i-mi2-datalab" class="titleslide slide level1" data-background="img/MI2_z_logiem.PNG"><h1>Grupa MI<sup>2</sup> i MI<sup>2</sup> DataLab</h1></section></section>
<section><section id="mlgensig-machine-learning-methods-for-building-the-integrated-genetic-signatures-ncn-opus-grant-201621bst602176" class="titleslide slide level1"><h1>“MLGenSig: Machine Learning Methods for building the Integrated Genetic Signatures” NCN Opus grant 2016/21/B/ST6/02176</h1></section></section>
<section><section id="terminologia-biologiczna" class="titleslide slide level1"><h1>Terminologia biologiczna</h1></section><section id="podstawowe-pojecia" class="slide level2" data-background="img/DNA3.PNG">
<h2>Podstawowe pojęcia</h2>
<ul>
<li class="fragment">Sonda mikromacierzy</li>
<li class="fragment">Ekspresja genu</li>
<li class="fragment">Metylacja DNA</li>
</ul>
</section></section>
<section><section id="nazwa" class="titleslide slide level1"><h1>Nazwa</h1></section><section id="section" class="slide level2" data-background="prezentacje_biala_fioletowa/Slajd8.PNG">
<h2></h2>
</section><section id="section-1" class="slide level2" data-background="prezentacje_biala_fioletowa/Slajd9.PNG">
<h2></h2>
</section><section id="section-2" class="slide level2" data-background="prezentacje_biala_fioletowa/Slajd10.PNG">
<h2></h2>
</section><section id="section-3" class="slide level2" data-background="prezentacje_biala_fioletowa/Slajd11.PNG">
<h2></h2>
</section><section id="section-4" class="slide level2" data-background="prezentacje_biala_fioletowa/Slajd12.PNG">
<h2></h2>
</section></section>
<section><section id="ekspresja" class="titleslide slide level1"><h1>Ekspresja</h1></section><section id="testowanie" class="slide level2">
<h2>Testowanie</h2>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">BRCA_exp[<span class="dv">1</span><span class="op">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">5</span>]</code></pre></div>
<pre><code> SUBTYPE AANAT AARSD1 AATF AATK
TCGA-A1-A0SB-01A-11R-A144-07 Normal 9 2354 2870 317
TCGA-A1-A0SD-01A-11R-A115-07 LumA 2 1846 5656 312
TCGA-A1-A0SE-01A-11R-A084-07 LumA 11 3391 9522 736
TCGA-A1-A0SF-01A-11R-A144-07 LumA 0 2169 4625 169
TCGA-A1-A0SG-01A-11R-A144-07 LumA 1 2273 3473 92</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">calculate_test</span>(data, condition, test)</code></pre></div>
<pre><code> id log2.fold pval mean_LumA mean_other mean
1 AURKB 2.339920 3.191000e-32 539.0426 2323.8868 1485.01
2 CBX2 2.895062 2.834335e-26 632.5106 4296.6038 2574.48
3 KPNA2 1.447288 8.551812e-24 11547.36 26427.38 19433.77
4 PRR11 3.822148 2.286874e-22 396.383 3479.981 2030.69
5 BIRC5 1.988998 1.953941e-21 1957.085 6658.358 4448.76
6 GSG2 1.405039 3.527773e-21 278.2128 629.3396 464.31</code></pre>
</section><section id="volcano-plot" class="slide level2">
<h2>Volcano plot</h2>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">plot_volcano</span>(data, line, names, fold_line)</code></pre></div>
<p><img src="img/volcano1.png" height='400'></p>
</section></section>
<section><section id="metylacja" class="titleslide slide level1"><h1>Metylacja</h1></section><section id="agregacja-sond-do-genow" class="slide level2">
<h2>Agregacja sond do genów</h2>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">BRCA_met[<span class="dv">1</span><span class="op">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">4</span>]</code></pre></div>
<pre><code> SUBTYPE cg00021527 cg00031162 cg00032227
TCGA-A1-A0SD-01A-11D-A112-05 LumA 0.03781858 0.7910348 0.006391233
TCGA-A2-A04N-01A-11D-A112-05 LumA 0.01437552 0.7359370 0.008752293
TCGA-A2-A04P-01A-31D-A032-05 Basal 0.01360124 0.6967802 0.009442039
TCGA-A2-A04Q-01A-21D-A032-05 Basal 0.01525656 0.5341244 0.014674247
TCGA-A2-A04T-01A-21D-A032-05 Basal 0.01167384 0.7378100 0.012251559</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">BRCA_met_gen <-<span class="st"> </span><span class="kw">aggregate_probes</span>(data) </code></pre></div>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">BRCA_met_gen[<span class="dv">1</span><span class="op">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">4</span>]</code></pre></div>
<pre><code> AANAT AARSD1 AATF AATK
TCGA-A1-A0SD-01A-11D-A112-05 0.7148533 0.8625816 0.24294092 0.7835302
TCGA-A2-A04N-01A-11D-A112-05 0.5850106 0.8355825 0.21367129 0.8466190
TCGA-A2-A04P-01A-31D-A032-05 0.4495537 0.8786166 0.03277413 0.3417919
TCGA-A2-A04Q-01A-21D-A032-05 0.7120650 0.8819490 0.03460160 0.7264985
TCGA-A2-A04T-01A-21D-A032-05 0.6010397 0.7739978 0.02501599 0.6276399</code></pre>
</section><section id="methylation-path" class="slide level2">
<h2>Methylation path</h2>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">plot_methylation_path</span>(data, condition, gene, show.gene, observ)</code></pre></div>
<p><img src="img/path1.png" height='400'></p>
</section><section id="testowanie-1" class="slide level2">
<h2>Testowanie</h2>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">calculate_test</span>(data, condition, test)</code></pre></div>
<pre><code> id log2.fold pval mean_LumA mean_other
1 ICAM2 -0.15151320 3.754116e-17 0.2547275 0.4062407
2 RILP -0.05073691 2.575168e-13 0.3079069 0.3586438
3 PIPOX 0.11505558 5.360053e-12 0.4242804 0.3092248
4 TNFSF12 -0.13412855 5.867083e-12 0.1791401 0.3132686
5 CD7 0.09822690 1.641919e-11 0.8635077 0.7652808</code></pre>
</section></section>
<section><section id="integracja-ekspresji-i-metylacji" class="titleslide slide level1"><h1>Integracja ekspresji i metylacji</h1></section><section id="tabela-porownan" class="slide level2">
<h2>Tabela porównań</h2>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">comparison <-<span class="st"> </span><span class="kw">calculate_comparison_table</span>(data1, data2, condition1,
condition2, test1, test2)</code></pre></div>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">head</span>(comparison)</code></pre></div>
<pre><code> id nbinom2.log2.fold nbinom2.pval ttest.log2.fold ttest.pval geom.mean.rank no.probes
59 AURKB 2.360714 1.704243e-37 0.0017389592 2.077252e-01 1.881527e-19 2
102 CBX2 2.905397 5.402147e-31 0.0584687549 1.214043e-06 8.098418e-19 2
327 KPNA2 1.466181 3.396674e-26 0.0012105971 7.505750e-01 1.596702e-13 1
277 GSG2 1.426569 3.325659e-25 -0.0018566938 2.411495e-01 2.831926e-13 2
66 BIRC5 2.004989 9.482155e-24 -0.0005444811 5.330216e-01 2.248153e-12 1
334 KRT16 4.333332 4.102956e-19 0.0486814033 1.606151e-05 2.567093e-12 2</code></pre>
</section><section id="volcano-plots" class="slide level2">
<h2>Volcano plots</h2>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">plot_volcanoes</span>(data.m, data.e,
condition.m, condition.e,
gene, test.m, test.e)</code></pre></div>
<p><img src="img/volcano2.png" height="400"></p>
</section><section id="informacje-dla-wybranego-genu" class="slide level2">
<h2>Informacje dla wybranego genu</h2>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">plot_gene</span>(data.m, data.e,
condition.m, condition.e,
gene, show.gene, observ, islands)</code></pre></div>
<p><img src="img/path2.png" height="400"></p>
</section><section id="section-5" class="slide level2" data-background="img/pomoce.PNG">
<h2></h2>
</section></section>
<section><section id="co-dalej" class="titleslide slide level1"><h1>Co dalej?</h1></section><section id="github" class="slide level2">
<h2>GitHub</h2>
<ul>
<li class="fragment"><a href="https://github.com/geneticsMiNIng/MLGenSig" class="uri">https://github.com/geneticsMiNIng/MLGenSig</a></li>
<li class="fragment"><a href="https://github.com/MI2DataLab" class="uri">https://github.com/MI2DataLab</a></li>
</ul>
</section></section>
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