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<!DOCTYPE html>
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<head>
<meta charset="utf-8">
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<title>RNAseq Using R Programming with R</title>
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<body class="lesson">
<div class="container card">
<div class="banner" align="right" style="margin-top: 5px">
<a href="http://monash.edu/bioinformatics" title="Monash Bioinformatics Platform">
<div style="margin-right: 5px;" class="label swc-blue-bg">Monash Bioinformatics Platform</div>
</a>
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<article>
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<div class="col-md-10 col-md-offset-1">
<a href="index.html"><h1 class="title">Programming with R</h1></a>
<h2 class="subtitle">Guide</h2>
<p>This lesson is written as an introduction to R, but its real purpose is to introduce the single most important idea in programming: how to solve problems by building functions, each of which can fit in a programmer’s working memory. In order to teach that, we must teach people a little about the mechanics of manipulating data with lists and file I/O so that their functions can do things they actually care about. Our teaching order tries to show practical uses of every idea as soon as it is introduced; instructors should resist the temptation to explain the “other 90%” of the language as well.</p>
<p>The secondary goal of this lesson is to give them a usable mental model of how programs run (what computer science educators call a <a href="reference.html#notional-machine">notional machine</a> so that they can debug things when they go wrong. In particular, they must understand how function call stacks work.</p>
<p>The final example asks them to build a command-line tool that works with the Unix pipe-and-filter model. We do this because it is a useful skill and because it helps learners see that the software they use isn’t magical. Tools like <code>grep</code> might be more sophisticated than the programs our learners can write at this point in their careers, but it’s crucial they realize this is a difference of scale rather than kind.</p>
<h2 id="teaching-notes">Teaching Notes</h2>
<ul>
<li><p>Watching the instructor grow programs step by step is as helpful to learners as anything to do with Python. Resist the urge to update a single cell repeatedly (which is what you’d probably do in real life). Instead, clone the previous cell and write the update in the new copy so that learners have a complete record of how the program grew. Once you’ve done this, you can say, “Now why don’t we just breaks things into small functions right from the start?”</p></li>
<li><p>The discussion of command-line scripts assumes that students understand standard I/O and building filters, which are covered in the lesson on the shell.</p></li>
</ul>
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</article>
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<a class="label swc-blue-bg" href="https://github.com/MonashBioinformaticsPlatform/RNAseq-DE-analysis-with-R">Source</a>
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