Merge branch 'master' of https://github.com/RockefellerUniversity/Int…

…ro_To_R_1Day

docs/presentations/singlepage/introToR_Session1.html

@@ -1557,8 +1557,8 @@
 
 
 <h1 class="title toc-ignore">Introduction to R - Session 1</h1>
-<h3 class="subtitle">Rockefeller UniversityBioinformatics Resource
-Center</h3>
+<h3 class="subtitle">Bioinformatics Resource Center - Rockefeller
+University</h3>
 <h4 class="author"><a href="http://rockefelleruniversity.github.io/Intro_To_R_1Day/" class="uri">http://rockefelleruniversity.github.io/Intro_To_R_1Day/</a></h4>
 <h4 class="author"><a href="mailto:brc@rockefeller.edu" class="email">brc@rockefeller.edu</a></h4>
 
@@ -3006,111 +3006,111 @@ <h2>Data from external sources</h2>
 Gene_a
 </td>
 <td style="text-align:right;">
-3.748015
+6.114098
 </td>
 <td style="text-align:right;">
-5.673906
+3.651662
 </td>
 <td style="text-align:right;">
-3.689673
+5.511621
 </td>
 </tr>
 <tr>
 <td style="text-align:left;">
 Gene_b
 </td>
 <td style="text-align:right;">
-3.911023
+4.789224
 </td>
 <td style="text-align:right;">
-3.511461
+4.942630
 </td>
 <td style="text-align:right;">
-4.741946
+2.725805
 </td>
 </tr>
 <tr>
 <td style="text-align:left;">
 Gene_c
 </td>
 <td style="text-align:right;">
-5.137442
+4.064273
 </td>
 <td style="text-align:right;">
-3.122917
+3.848893
 </td>
 <td style="text-align:right;">
-3.095816
+4.002280
 </td>
 </tr>
 <tr>
 <td style="text-align:left;">
 Gene_d
 </td>
 <td style="text-align:right;">
-3.885018
+4.536295
 </td>
 <td style="text-align:right;">
-3.694877
+5.752390
 </td>
 <td style="text-align:right;">
-3.145632
+3.339089
 </td>
 </tr>
 <tr>
 <td style="text-align:left;">
 Gene_e
 </td>
 <td style="text-align:right;">
-10.060803
+10.515184
 </td>
 <td style="text-align:right;">
-9.905741
+10.765139
 </td>
 <td style="text-align:right;">
-10.607116
+10.102932
 </td>
 </tr>
 <tr>
 <td style="text-align:left;">
 Gene_f
 </td>
 <td style="text-align:right;">
-9.540471
+8.991736
 </td>
 <td style="text-align:right;">
-9.757122
+9.843564
 </td>
 <td style="text-align:right;">
-9.828682
+11.131524
 </td>
 </tr>
 <tr>
 <td style="text-align:left;">
 Gene_g
 </td>
 <td style="text-align:right;">
-10.430112
+10.599208
 </td>
 <td style="text-align:right;">
-10.612781
+10.197178
 </td>
 <td style="text-align:right;">
-10.504008
+11.135410
 </td>
 </tr>
 <tr>
 <td style="text-align:left;">
 Gene_h
 </td>
 <td style="text-align:right;">
-12.648962
+10.055203
 </td>
 <td style="text-align:right;">
-10.484571
+8.363906
 </td>
 <td style="text-align:right;">
-10.413815
+9.181689
 </td>
 </tr>
 </tbody>

docs/presentations/singlepage/introToR_Session2.html

@@ -13,7 +13,7 @@
 <meta name="author" content="brc@rockefeller.edu" />
 
 
-<title>Introduction to R - Session 2</title>
+<title>Introduction to R - Session 1</title>
 
 <script>// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
 // be compatible with the behavior of Pandoc < 2.8).
@@ -1556,9 +1556,9 @@
 
 
 
-<h1 class="title toc-ignore">Introduction to R - Session 2</h1>
-<h3 class="subtitle">Rockefeller UniversityBioinformatics Resource
-Center</h3>
+<h1 class="title toc-ignore">Introduction to R - Session 1</h1>
+<h3 class="subtitle">Bioinformatics Resource Center - Rockefeller
+University</h3>
 <h4 class="author"><a href="http://rockefelleruniversity.github.io/Intro_To_R_1Day/" class="uri">http://rockefelleruniversity.github.io/Intro_To_R_1Day/</a></h4>
 <h4 class="author"><a href="mailto:brc@rockefeller.edu" class="email">brc@rockefeller.edu</a></h4>
 
@@ -2390,8 +2390,8 @@ <h2>Custom function example</h2>
 <span id="cb156-10"><a href="#cb156-10" aria-hidden="true" tabindex="-1"></a>A <span class="ot">&lt;-</span> <span class="fu">rnorm</span>(<span class="dv">20</span>)</span>
 <span id="cb156-11"><a href="#cb156-11" aria-hidden="true" tabindex="-1"></a></span>
 <span id="cb156-12"><a href="#cb156-12" aria-hidden="true" tabindex="-1"></a><span class="fu">my_zscore</span>(<span class="at">my_number=</span>A[<span class="dv">1</span>], <span class="at">my_vector=</span>A)</span></code></pre></div>
-<pre><code>## Mean is -0.339070410259268</code></pre>
-<pre><code>## [1] -0.9170779</code></pre>
+<pre><code>## Mean is -0.0201830063325983</code></pre>
+<pre><code>## [1] -0.2216552</code></pre>
 </div>
 <div id="debugging-functions" class="section level2">
 <h2>Debugging functions</h2>
@@ -2406,10 +2406,10 @@ <h2>Debugging functions</h2>
 <h2>Custom functions and apply</h2>
 <p>These custom functions can also be utilized with apply.</p>
 <div class="sourceCode" id="cb160"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb160-1"><a href="#cb160-1" aria-hidden="true" tabindex="-1"></a><span class="fu">sapply</span>(A, my_zscore, <span class="at">my_vector=</span>A)</span></code></pre></div>
-<pre><code>##  [1] -0.91707786 -1.27881585 -0.09207309  0.27502420 -0.21778697 -1.07329500
-##  [7] -0.01765323  0.16428822  1.18594526 -0.95894849 -0.02403633 -1.81818368
-## [13] -0.44579057  0.82992612  1.94427763 -0.03240710 -0.83499881  0.49418623
-## [19]  1.38393290  1.43348640</code></pre>
+<pre><code>##  [1] -0.22165519 -0.02666109 -0.23117481 -1.12656796 -1.23976279  0.40392274
+##  [7]  1.01395924 -1.76383043  1.65926044  1.38274371  0.19660351 -1.77719943
+## [13]  1.29564823 -0.72245280  0.53405124  0.97852803 -0.58430227  0.03153533
+## [19]  0.34436005 -0.14700574</code></pre>
 </div>
 </div>
 <div id="getting-additional-libraries" class="section level1">

docs/presentations/slides/introToR_Session1.html

@@ -16,7 +16,7 @@
 # Introduction to R - Session 1
 ]
 .subtitle[
-## Rockefeller UniversityBioinformatics Resource Center
+## Bioinformatics Resource Center - Rockefeller University
 ]
 .author[
 ### <a href="http://rockefelleruniversity.github.io/Intro_To_R_1Day/" class="uri">http://rockefelleruniversity.github.io/Intro_To_R_1Day/</a>
@@ -2561,51 +2561,51 @@
 &lt;tbody&gt;
   &lt;tr&gt;
    &lt;td style="text-align:left;"&gt; Gene_a &lt;/td&gt;
-   &lt;td style="text-align:right;"&gt; 4.677695 &lt;/td&gt;
-   &lt;td style="text-align:right;"&gt; 2.407734 &lt;/td&gt;
-   &lt;td style="text-align:right;"&gt; 4.688860 &lt;/td&gt;
+   &lt;td style="text-align:right;"&gt; 4.549640 &lt;/td&gt;
+   &lt;td style="text-align:right;"&gt; 4.055915 &lt;/td&gt;
+   &lt;td style="text-align:right;"&gt; 5.473899 &lt;/td&gt;
   &lt;/tr&gt;
   &lt;tr&gt;
    &lt;td style="text-align:left;"&gt; Gene_b &lt;/td&gt;
-   &lt;td style="text-align:right;"&gt; 4.206249 &lt;/td&gt;
-   &lt;td style="text-align:right;"&gt; 3.540387 &lt;/td&gt;
-   &lt;td style="text-align:right;"&gt; 4.031366 &lt;/td&gt;
+   &lt;td style="text-align:right;"&gt; 4.061181 &lt;/td&gt;
+   &lt;td style="text-align:right;"&gt; 4.567089 &lt;/td&gt;
+   &lt;td style="text-align:right;"&gt; 2.627906 &lt;/td&gt;
   &lt;/tr&gt;
   &lt;tr&gt;
    &lt;td style="text-align:left;"&gt; Gene_c &lt;/td&gt;
-   &lt;td style="text-align:right;"&gt; 4.369869 &lt;/td&gt;
-   &lt;td style="text-align:right;"&gt; 5.892023 &lt;/td&gt;
-   &lt;td style="text-align:right;"&gt; 3.488333 &lt;/td&gt;
+   &lt;td style="text-align:right;"&gt; 3.768581 &lt;/td&gt;
+   &lt;td style="text-align:right;"&gt; 3.002469 &lt;/td&gt;
+   &lt;td style="text-align:right;"&gt; 3.166941 &lt;/td&gt;
   &lt;/tr&gt;
   &lt;tr&gt;
    &lt;td style="text-align:left;"&gt; Gene_d &lt;/td&gt;
-   &lt;td style="text-align:right;"&gt; 2.946114 &lt;/td&gt;
-   &lt;td style="text-align:right;"&gt; 3.191295 &lt;/td&gt;
-   &lt;td style="text-align:right;"&gt; 3.486030 &lt;/td&gt;
+   &lt;td style="text-align:right;"&gt; 4.020130 &lt;/td&gt;
+   &lt;td style="text-align:right;"&gt; 4.633432 &lt;/td&gt;
+   &lt;td style="text-align:right;"&gt; 4.570594 &lt;/td&gt;
   &lt;/tr&gt;
   &lt;tr&gt;
    &lt;td style="text-align:left;"&gt; Gene_e &lt;/td&gt;
-   &lt;td style="text-align:right;"&gt; 10.616482 &lt;/td&gt;
-   &lt;td style="text-align:right;"&gt; 11.044152 &lt;/td&gt;
-   &lt;td style="text-align:right;"&gt; 8.989242 &lt;/td&gt;
+   &lt;td style="text-align:right;"&gt; 9.302783 &lt;/td&gt;
+   &lt;td style="text-align:right;"&gt; 9.623047 &lt;/td&gt;
+   &lt;td style="text-align:right;"&gt; 9.761798 &lt;/td&gt;
   &lt;/tr&gt;
   &lt;tr&gt;
    &lt;td style="text-align:left;"&gt; Gene_f &lt;/td&gt;
-   &lt;td style="text-align:right;"&gt; 8.859909 &lt;/td&gt;
-   &lt;td style="text-align:right;"&gt; 10.061845 &lt;/td&gt;
-   &lt;td style="text-align:right;"&gt; 9.814015 &lt;/td&gt;
+   &lt;td style="text-align:right;"&gt; 9.505908 &lt;/td&gt;
+   &lt;td style="text-align:right;"&gt; 9.555179 &lt;/td&gt;
+   &lt;td style="text-align:right;"&gt; 9.795322 &lt;/td&gt;
   &lt;/tr&gt;
   &lt;tr&gt;
    &lt;td style="text-align:left;"&gt; Gene_g &lt;/td&gt;
-   &lt;td style="text-align:right;"&gt; 9.477750 &lt;/td&gt;
-   &lt;td style="text-align:right;"&gt; 10.645196 &lt;/td&gt;
-   &lt;td style="text-align:right;"&gt; 11.669200 &lt;/td&gt;
+   &lt;td style="text-align:right;"&gt; 9.919977 &lt;/td&gt;
+   &lt;td style="text-align:right;"&gt; 8.395819 &lt;/td&gt;
+   &lt;td style="text-align:right;"&gt; 10.455944 &lt;/td&gt;
   &lt;/tr&gt;
   &lt;tr&gt;
    &lt;td style="text-align:left;"&gt; Gene_h &lt;/td&gt;
-   &lt;td style="text-align:right;"&gt; 11.291157 &lt;/td&gt;
-   &lt;td style="text-align:right;"&gt; 9.920510 &lt;/td&gt;
-   &lt;td style="text-align:right;"&gt; 11.632775 &lt;/td&gt;
+   &lt;td style="text-align:right;"&gt; 10.139262 &lt;/td&gt;
+   &lt;td style="text-align:right;"&gt; 8.447773 &lt;/td&gt;
+   &lt;td style="text-align:right;"&gt; 10.196103 &lt;/td&gt;
   &lt;/tr&gt;
 &lt;/tbody&gt;
 &lt;/table&gt;

docs/presentations/slides/introToR_Session2.html

@@ -1,7 +1,7 @@
 <!DOCTYPE html>
 <html lang="" xml:lang="">
   <head>
-    <title>Introduction to R - Session 2</title>
+    <title>Introduction to R - Session 1</title>
     <meta charset="utf-8" />
     <meta name="author" content="http://rockefelleruniversity.github.io/Intro_To_R_1Day/" />
     <meta name="author" content="brc@rockefeller.edu" />
@@ -13,10 +13,10 @@
 class: center, middle, inverse, title-slide
 
 .title[
-# Introduction to R - Session 2
+# Introduction to R - Session 1
 ]
 .subtitle[
-## Rockefeller UniversityBioinformatics Resource Center
+## Bioinformatics Resource Center - Rockefeller University
 ]
 .author[
 ### <a href="http://rockefelleruniversity.github.io/Intro_To_R_1Day/" class="uri">http://rockefelleruniversity.github.io/Intro_To_R_1Day/</a>
@@ -1388,11 +1388,11 @@
 ```
 
 ```
-## Mean is 0.149024753492524
+## Mean is -0.0305961131565969
 ```
 
 ```
-## [1] 0.5638451
+## [1] -0.9496808
 ```
 
 ---
@@ -1417,10 +1417,10 @@
 ```
 
 ```
-##  [1]  0.56384513 -0.07913317 -0.32825886 -0.14149073  0.40815142 -1.96228103
-##  [7]  1.35650407 -0.04022448  0.84512579 -1.10856172  0.84198288  0.15306034
-## [13]  0.89895322  0.90852486 -0.67683044  0.32560389 -1.05653992 -0.52221068
-## [19]  1.58908816 -1.97530874
+##  [1] -0.94968075 -0.78305717  1.05352700  0.06490175 -0.75293440 -0.23613690
+##  [7]  1.94375837 -0.03252430 -1.36864893 -0.98164156 -1.22428793  1.04927928
+## [13] -1.10757287  0.92592627 -0.88102207 -0.19882759  0.24303620  0.85178392
+## [19]  1.24578852  1.13833316
 ```