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Jasmine Gu committed Jan 17, 2025
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2 changes: 1 addition & 1 deletion .nojekyll
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38 changes: 13 additions & 25 deletions Procedure1.html
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<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">


<title>2&nbsp; Procedure 1 – ClassifyR PlayBook</title>
<title>2&nbsp; Comparing cross-validated results – ClassifyR PlayBook</title>
<style>
code{white-space: pre-wrap;}
span.smallcaps{font-variant: small-caps;}
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<script src="site_libs/quarto-search/fuse.min.js"></script>
<script src="site_libs/quarto-search/quarto-search.js"></script>
<meta name="quarto:offset" content="./">
<link href="./Procedure2.html" rel="next">
<link href="./Procedure3.html" rel="next">
<link href="./index.html" rel="prev">
<script src="site_libs/quarto-html/quarto.js"></script>
<script src="site_libs/quarto-html/popper.min.js"></script>
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<button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" role="button" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
<i class="bi bi-layout-text-sidebar-reverse"></i>
</button>
<nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="./Procedure1.html"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Procedure 1</span></a></li></ol></nav>
<nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="./Procedure1.html"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Comparing cross-validated results</span></a></li></ol></nav>
<a class="flex-grow-1" role="navigation" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
</a>
<button type="button" class="btn quarto-search-button" aria-label="Search" onclick="window.quartoOpenSearch();">
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<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./Procedure1.html" class="sidebar-item-text sidebar-link active">
<span class="menu-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Procedure 1</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./Procedure2.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">Procedure 2</span></span></a>
<span class="menu-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Comparing cross-validated results</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./Procedure3.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">4</span>&nbsp; <span class="chapter-title">Procedure 3</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./Procedure4.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">5</span>&nbsp; <span class="chapter-title">Procedure 4</span></span></a>
<span class="menu-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">Multi-Platform Precision Pathway</span></span></a>
</div>
</li>
</ul>
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<h2 id="toc-title">Table of contents</h2>

<ul>
<li><a href="#intro" id="toc-intro" class="nav-link active" data-scroll-target="#intro"><span class="header-section-number">2.1</span> Intro</a></li>
<li><a href="#introduction" id="toc-introduction" class="nav-link active" data-scroll-target="#introduction"><span class="header-section-number">2.1</span> Introduction</a></li>
<li><a href="#set-up-the-environment-and-data-objects" id="toc-set-up-the-environment-and-data-objects" class="nav-link" data-scroll-target="#set-up-the-environment-and-data-objects"><span class="header-section-number">2.2</span> Set up the environment and data objects</a></li>
<li><a href="#cross-validated-classification" id="toc-cross-validated-classification" class="nav-link" data-scroll-target="#cross-validated-classification"><span class="header-section-number">2.3</span> Cross-validated Classification</a></li>
<li><a href="#classification-evaluation" id="toc-classification-evaluation" class="nav-link" data-scroll-target="#classification-evaluation"><span class="header-section-number">2.4</span> Classification Evaluation</a></li>
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<header id="title-block-header" class="quarto-title-block default">
<div class="quarto-title">
<h1 class="title"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Procedure 1</span></h1>
<h1 class="title"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Comparing cross-validated results</span></h1>
</div>


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</header>


<section id="intro" class="level2" data-number="2.1">
<h2 data-number="2.1" class="anchored" data-anchor-id="intro"><span class="header-section-number">2.1</span> Intro</h2>
<p>Procedure 1 aims to compare the classification sample accuracy of breast cancer subtypes using bulk gene expression data and histologically predicted gene expression data. Sample accuracy is defined as the proportion of correctly predicted classifications over multiple repeats. For example, if 70 out of 100 repeats correctly classify an individual, their sample accuracy is 0.70.</p>
<section id="introduction" class="level2" data-number="2.1">
<h2 data-number="2.1" class="anchored" data-anchor-id="introduction"><span class="header-section-number">2.1</span> Introduction</h2>
<p>Procedure 1 aims to compare the sample accuracy of breast cancer subtype classification using bulk gene expression data and histologically predicted gene expression data. Sample accuracy is defined as the proportion of correctly predicted classifications over multiple repeats. For example, if 70 out of 100 repeats correctly classify an individual, their sample accuracy is 0.70.</p>
<p>This analysis involves 54 oestrogen receptor-positive (ER+) and progesterone receptor-positive (PR+) breast cancer patients, with each assay containing expression values for 268 genes. The classification outcomes are ‘Subtype 1’ and ‘Subtype 2’, found by unsupervised machine learning. Subtype 1 corresponds to patients with higher expression of LPL, CAVIN2, and TIMP4 in macrophage cells, and ADIPOQ in stromal cells, associated with better survival. Subtype 2 is the opposite, associated with poorer survival. More details on the subtypes can be found at https://www.biorxiv.org/content/10.1101/2024.07.02.601790v1.full.</p>
</section>
<section id="set-up-the-environment-and-data-objects" class="level2" data-number="2.2">
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<div class="cell">
<div class="sourceCode cell-code" id="cb1"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(ClassifyR)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<p><code>ClassifyR</code> is used to perform all the demonstrated analyses with <code>openxlsx</code> only used to read in data.</p>
<p><code>ClassifyR</code> is used to perform all the demonstrated analyses.</p>
<p><strong>2. Import preprocessed datasets for analysis</strong></p>
<p><span style="color: grey;">Timing ~ 0.04s</span></p>
<div class="cell">
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</a>
</div>
<div class="nav-page nav-page-next">
<a href="./Procedure2.html" class="pagination-link" aria-label="Procedure 2">
<span class="nav-page-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">Procedure 2</span></span> <i class="bi bi-arrow-right-short"></i>
<a href="./Procedure3.html" class="pagination-link" aria-label="Multi-Platform Precision Pathway">
<span class="nav-page-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">Multi-Platform Precision Pathway</span></span> <i class="bi bi-arrow-right-short"></i>
</a>
</div>
</nav>
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