RCourse/R-Course.html at master · DLWheeler/RCourse · GitHub

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<div id="a-short-course-in-r-for-biologists" class="section level1">
<h1>A Short Course in R for Biologists</h1>
<p><em>“A Short Course in R for Biologists”</em> is a one-day course given in four three-hour sessions entitled: <em>Introduction to R and Introduction to Bioconductor.</p>
<hr />
<blockquote>
<p><strong>No Registration Required</strong><br /><strong>Date &amp; Time:</strong> Tuesday, 22 November 2016 - 9:30am - 4:30pm<br /><strong>Location:</strong> FAES Classroom 4<br /><strong>Presenter:</strong> David Wheeler<br /><strong>Affiliations:</strong> Laboratory of Biochemistry and Molecular Biology/NCI <br /><strong>Format:</strong> Lecture/Hands-On</p>
</blockquote>
<hr />
<table>
<thead>
<tr class="header">
<th align="left">Day</th>
<th align="left">Morning Session, 9:30 AM-12:30 PM</th>
<th align="left">Afternoon Session, 1:30 PM-4:30 PM</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td align="left">Jan 29</td>
<td align="left"><em>Introduction to R</em></td>
<td align="left"><em>Introduction to Bioconductor</em></td>
</tr>
</tbody>
</table>
<p>The course will include frequent, short hands-on periods so students should bring their own laptops with a working installation of <em>R</em>, <strong>version 3.3 or later</strong>. In addition, several <em>R</em> packages will be used which must be installed prior to the course.</p>
<p><em>R</em> is a console application. Students who prefer a more graphically-oriented working environment will find that using <em>RStudio</em> as an environment in which to run <em>R</em> makes life much easier. If you are comfortable running programs, viewing output, and editing files at the terminal, you will not need <em>RStudio</em> in order to take the course. However, <em>RStudio</em> offers quite an array of functions that you may still find useful and it is well worth a look.</p>
<div id="r-installation" class="section level4">
<h4>R Installation</h4>
<p>The R program and instructions for its installation under Linux, Mac OSX, and Windows can be found here:</p>
<blockquote>
<p><a href="http://cran.r-project.org/">http://cran.r-project.org/</a></p>
</blockquote>
</div>
<div id="bioconductor-and-bioconductor-package-installation" class="section level4">
<h4>Bioconductor and Bioconductor Package Installation</h4>
<p>Complete instructions for the installation of the basic and additional <em>Bioconductor</em> packages are found here:</p>
<blockquote>
<p><a href="http://www.bioconductor.org/install/">http://www.bioconductor.org/install/</a></p>
</blockquote>
<p>In addition to the basic <em>Bioconductor</em> package, please install these additional <em>Bioconductor</em> packages prior to the start of the class:</p>
<table>
<tbody>
<tr class="odd">
<td align="left"><em>Biostrings</em></td>
<td align="left"><em>BSgenome</em></td>
<td align="left"><em>BSgenome.Celegans.UCSC.ce6</em></td>
</tr>
<tr class="even">
<td align="left"><em>TxDb.Celegans.UCSC.ce6.ensGene</em></td>
<td align="left"><em>GenomicFeatures</em></td>
<td align="left"><em>GenomicRanges</em></td>
</tr>
<tr class="odd">
<td align="left"><em>GenomicAlignments</em></td>
<td align="left"><em>TxDb.Hsapiens.UCSC.hg19.knownGene</em></td>
</tr>
</tbody>
</table>
<p>Briefly, the following code, executed from within an R session, should serve to install the basic <em>Bioconductor</em> package as well as the additional packages listed above:</p>
<pre><code># First, download the Bioconductor installer, biocLite()

source(&quot;http://bioconductor.org/biocLite.R&quot;)

# Now, use the installer to install several packages at once
# The base package, Biobase, will be installed automatically

biocLite(pkgs=c(&quot;Biostrings&quot;, &quot;BSgenome&quot;, &quot;BSgenome.Celegans.UCSC.ce6&quot;, &quot;TxDb.Celegans.UCSC.ce6.ensGene&quot;, &quot;GenomicFeatures&quot;, &quot;GenomicRanges&quot;, &quot;GenomicAlignments&quot;, &quot;TxDb.Hsapiens.UCSC.hg19.knownGene&quot;))</code></pre>
</div>
<div id="rstudio-installation" class="section level4">
<h4>RStudio Installation</h4>
<p>Install the “Desktop, Open Source Edition”:</p>
<blockquote>
<p><a href="http://www.rstudio.com/products/RStudio/#Desk">http://www.rstudio.com/products/RStudio/#Desk</a></p>
</blockquote>
</div>
<div id="class-outline" class="section level2">
<h2>Class Outline</h2>
<div id="day-1-jan-29-morning-session-introduction-to-r" class="section level3">
<h3>Day 1 (Nov 22), Morning Session: Introduction to R</h3>
<ul>
<li>The R environment
<ul>
<li>Starting an R Session, Setting Options</li>
<li>Listing Variables, Editing Commands, Using the R History</li>
<li>Getting Help on an R Function</li>
<li>Logging a Session to a File</li>
<li>Running External R Code</li>
<li>Installing and Loading Packages</li>
<li>Ending a Session, Saving Your Work</li>
</ul></li>
<li>The Elements of R
<ul>
<li>Numeric</li>
<li>Character<br /></li>
<li>Logical</li>
<li>Missing Values</li>
</ul></li>
<li>R Data Structures
<ul>
<li>Vectors</li>
<li>Matrices</li>
<li>Lists</li>
<li>Data.Frames</li>
<li>Factors</li>
<li>Functions</li>
<li>Other Complex Structures</li>
</ul></li>
<li>Procedures
<ul>
<li>Reading and Writing Data</li>
<li>Exploring and Summarizing Data</li>
<li>Dealing with Missing Data</li>
<li>Restructuring Data</li>
<li>Relabeling Data</li>
<li>Subsetting Data</li>
<li>Operating on Rows or Columns of Data</li>
<li>Saving R Objects for Later Use</li>
<li>Graphing Data</li>
<li>Simple Statistical Tests</li>
<li>Example: A Simple Analysis of Probe Intensity Data</li>
</ul></li>
<li>Project: Creating a Graphical Function in 4 Easy Steps
<ul>
<li>Step 1: Create a Heatmap of Gene Expression Data</li>
<li>Step 2: Package Heatmap as a Function</li>
<li>Step 3: Add some Custom Formatting</li>
<li>Step 4: Save for Future Use and – Voila, You Have Created your own Heatmap Library!</li>
</ul></li>
</ul>
</div>
<div id="day-1-nov-22-afternoon-session-introduction-to-bioconductor" class="section level3">
<h3>Day 1 (Nov 22), Afternoon Session: Introduction to Bioconductor</h3>
<ul>
<li>Installing Bioconductor</li>
<li>An Overview of Bioconductor Packages</li>
<li>Fundamental Packages
<ul>
<li>Biobase: the Foundation</li>
<li>Biostrings: A Representation of Biological Sequences</li>
<li>BSgenome: A Representation of Complete Genomic Sequences</li>
<li>GenomicRanges: Manipulation of Genomic Intervals</li>
<li>GenomicFeatures: Manipulation of Genomic Features</li>
<li>GenomicAlgnments: Manipulation of Short Genomic Alignments</li>
</ul></li>
<li>Two Fundamental Structures to Contain Experiment Data
<ul>
<li>The ExpressionSet for Array Data
<ul>
<li>Constructing an ExpressionSet</li>
<li>Analyzing an ExpressionSet</li>
</ul></li>
<li>The SummarizedExperiment for NGS Sequence Data
<ul>
<li>Constructing a SummarizedExperiment</li>
<li>Analyzing a SummarizedExperiment</li>
</ul></li>
</ul></li>
</ul>
</div>


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