Update documentation

Author: gaow

Main_Figures/Figure_2/index.html

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     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>Figure 2\n\nAnalysis and results for Figure 2. &#8212; Data and code to reproduce figures in ColocBoost manuscript</title>
+    <title>Figure 2 &#8212; Data and code to reproduce figures in ColocBoost manuscript</title>
 
 
 
@@ -32,7 +32,7 @@
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@@ -63,7 +63,7 @@
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     <link rel="next" title="Figure 2a. Statistical power and False Discovery Rate (FDR) comparisons." href="Figure_2a.html" />
-    <link rel="prev" title="Main Figures\n\nThis section contains the main figures from our analysis." href="../index.html" />
+    <link rel="prev" title="Main Figures" href="../index.html" />
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@@ -171,21 +171,21 @@
         <ul class="nav bd-sidenav bd-sidenav__home-link">
             <li class="toctree-l1">
                 <a class="reference internal" href="../../index.html">
-                    ColocBoost Manuscript Companion Resources\n\nCode and data to reproduce figures in ColocBoost manuscript.
+                    ColocBoost Manuscript Companion Resources
                 </a>
             </li>
         </ul>
         <ul class="current nav bd-sidenav">
-<li class="toctree-l1 current active has-children"><a class="reference internal" href="../index.html">Main Figures\n\nThis section contains the main figures from our analysis.</a><details open="open"><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul class="current">
-<li class="toctree-l2 current active has-children"><a class="current reference internal" href="#">Figure 2\n\nAnalysis and results for Figure 2.</a><details open="open"><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
+<li class="toctree-l1 current active has-children"><a class="reference internal" href="../index.html">Main Figures</a><details open="open"><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul class="current">
+<li class="toctree-l2 current active has-children"><a class="current reference internal" href="#">Figure 2</a><details open="open"><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
 <li class="toctree-l3"><a class="reference internal" href="Figure_2a.html">Figure 2a. Statistical power and False Discovery Rate (FDR) comparisons.</a></li>
 <li class="toctree-l3"><a class="reference internal" href="Figure_2b.html">Figure 2b. Representative simulation examples.</a></li>
 <li class="toctree-l3"><a class="reference internal" href="Figure_2c.html">Figure 2c. Variant‐level precision‐recall curves.</a></li>
 <li class="toctree-l3"><a class="reference internal" href="Figure_2d.html">Figure 2d. Statistical power and False Discovery Rate (FDR) comparisons.</a></li>
 <li class="toctree-l3"><a class="reference internal" href="Figure_2e.html">Figure 2e. Statistical power and False Discovery Rate (FDR) comparisons.</a></li>
 </ul>
 </details></li>
-<li class="toctree-l2 has-children"><a class="reference internal" href="../Figure_3/index.html">Figure 3\n\nAnalysis and results for Figure 3.</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
+<li class="toctree-l2 has-children"><a class="reference internal" href="../Figure_3/index.html">Figure 3</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
 <li class="toctree-l3"><a class="reference internal" href="../Figure_3/Figure_3a.html">Figure 3a. Colocalization patterns across three different molecular trait modalities (expression, splicing, protein abundance).</a></li>
 <li class="toctree-l3"><a class="reference internal" href="../Figure_3/Figure_3b.html">Figure 3b. Distribution of the number of 95% CoSs corresponding to the different numbers of colocalized traits per locus.</a></li>
 
@@ -198,19 +198,19 @@
 <li class="toctree-l3"><a class="reference internal" href="../Figure_3/Figure_3i.html">Figure 3i. Shared cell-types in primary CoS and secondary CoS.</a></li>
 </ul>
 </details></li>
-<li class="toctree-l2 has-children"><a class="reference internal" href="../Figure_4/index.html">Figure 4\n\nAnalysis and results for Figure 4.</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
+<li class="toctree-l2 has-children"><a class="reference internal" href="../Figure_4/index.html">Figure 4</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
 <li class="toctree-l3"><a class="reference internal" href="../Figure_4/Figure_4a.html">Figure 4a. Variant set -level Excess-of-overlap (EOO) analysis.</a></li>
 <li class="toctree-l3"><a class="reference internal" href="../Figure_4/Figure_4b.html">Figure 4b. Variant set -level Excess-of-overlap (EOO) analysis in bulk region.</a></li>
 <li class="toctree-l3"><a class="reference internal" href="../Figure_4/Figure_4c.html">Figure 4c. Variant set -level Excess-of-overlap (EOO) analysis in cell types.</a></li>
 <li class="toctree-l3"><a class="reference internal" href="../Figure_4/Figure_4d.html">Figure 4d. Microglia-specific eQTL colocalization in FCGR2A.</a></li>
 </ul>
 </details></li>
-<li class="toctree-l2 has-children"><a class="reference internal" href="../Figure_5/index.html">Figure 5\n\nAnalysis and results for Figure 5.</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
+<li class="toctree-l2 has-children"><a class="reference internal" href="../Figure_5/index.html">Figure 5</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
 <li class="toctree-l3"><a class="reference internal" href="../Figure_5/Figure_5abc.html">Figure 5abc. Disease heritability analyses of variant-level functional annotations derived from ColocBoost.</a></li>
 <li class="toctree-l3"><a class="reference internal" href="../Figure_5/Figure_5d.html">Figure 5d. Standardized effect sizes of the MaxVCP-xQTL and an analogous score based on the HyPrColoc method.</a></li>
 </ul>
 </details></li>
-<li class="toctree-l2 has-children"><a class="reference internal" href="../Figure_6/index.html">Figure 6\n\nAnalysis and results for Figure 6.</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
+<li class="toctree-l2 has-children"><a class="reference internal" href="../Figure_6/index.html">Figure 6</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
 <li class="toctree-l3"><a class="reference internal" href="../Figure_6/Figure_6a.html">Figure 6a. UpSet plot comparison.</a></li>
 <li class="toctree-l3"><a class="reference internal" href="../Figure_6/Figure_6b.html">Figure 6b. Scatter plot across variants in terms of the magnitude of quantile-matched z-scores.</a></li>
 <li class="toctree-l3"><a class="reference internal" href="../Figure_6/Figure_6c.html">Figure 6c. Distribution of distances from the gene TSS for CoS.</a></li>
@@ -405,7 +405,7 @@
 
 
 <div id="jb-print-docs-body" class="onlyprint">
-    <h1>Figure 2\n\nAnalysis and results for Figure 2.</h1>
+    <h1>Figure 2</h1>
     <!-- Table of contents -->
     <div id="print-main-content">
         <div id="jb-print-toc">
@@ -419,8 +419,9 @@ <h1>Figure 2\n\nAnalysis and results for Figure 2.</h1>
 <div id="searchbox"></div>
                 <article class="bd-article">
 
-  <section class="tex2jax_ignore mathjax_ignore" id="figure-2-n-nanalysis-and-results-for-figure-2">
-<h1>Figure 2\n\nAnalysis and results for Figure 2.<a class="headerlink" href="#figure-2-n-nanalysis-and-results-for-figure-2" title="Link to this heading">#</a></h1>
+  <section class="tex2jax_ignore mathjax_ignore" id="figure-2">
+<h1>Figure 2<a class="headerlink" href="#figure-2" title="Link to this heading">#</a></h1>
+<p>Analysis and results for Figure 2.</p>
 <div class="toctree-wrapper compound">
 </div>
 </section>
@@ -461,7 +462,7 @@ <h1>Figure 2\n\nAnalysis and results for Figure 2.<a class="headerlink" href="#f
       <i class="fa-solid fa-angle-left"></i>
       <div class="prev-next-info">
         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">Main Figures\n\nThis section contains the main figures from our analysis.</p>
+        <p class="prev-next-title">Main Figures</p>
       </div>
     </a>
     <a class="right-next"

Main_Figures/Figure_3/index.html

@@ -8,7 +8,7 @@
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     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>Figure 3\n\nAnalysis and results for Figure 3. &#8212; Data and code to reproduce figures in ColocBoost manuscript</title>
+    <title>Figure 3 &#8212; Data and code to reproduce figures in ColocBoost manuscript</title>
 
 
 
@@ -32,7 +32,7 @@
     <link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-book-theme.css?v=eba8b062" />
     <link rel="stylesheet" type="text/css" href="../../_static/togglebutton.css?v=13237357" />
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+    <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
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@@ -171,21 +171,21 @@
         <ul class="nav bd-sidenav bd-sidenav__home-link">
             <li class="toctree-l1">
                 <a class="reference internal" href="../../index.html">
-                    ColocBoost Manuscript Companion Resources\n\nCode and data to reproduce figures in ColocBoost manuscript.
+                    ColocBoost Manuscript Companion Resources
                 </a>
             </li>
         </ul>
         <ul class="current nav bd-sidenav">
-<li class="toctree-l1 current active has-children"><a class="reference internal" href="../index.html">Main Figures\n\nThis section contains the main figures from our analysis.</a><details open="open"><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul class="current">
-<li class="toctree-l2 has-children"><a class="reference internal" href="../Figure_2/index.html">Figure 2\n\nAnalysis and results for Figure 2.</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
+<li class="toctree-l1 current active has-children"><a class="reference internal" href="../index.html">Main Figures</a><details open="open"><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul class="current">
+<li class="toctree-l2 has-children"><a class="reference internal" href="../Figure_2/index.html">Figure 2</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
 <li class="toctree-l3"><a class="reference internal" href="../Figure_2/Figure_2a.html">Figure 2a. Statistical power and False Discovery Rate (FDR) comparisons.</a></li>
 <li class="toctree-l3"><a class="reference internal" href="../Figure_2/Figure_2b.html">Figure 2b. Representative simulation examples.</a></li>
 <li class="toctree-l3"><a class="reference internal" href="../Figure_2/Figure_2c.html">Figure 2c. Variant‐level precision‐recall curves.</a></li>
 <li class="toctree-l3"><a class="reference internal" href="../Figure_2/Figure_2d.html">Figure 2d. Statistical power and False Discovery Rate (FDR) comparisons.</a></li>
 <li class="toctree-l3"><a class="reference internal" href="../Figure_2/Figure_2e.html">Figure 2e. Statistical power and False Discovery Rate (FDR) comparisons.</a></li>
 </ul>
 </details></li>
-<li class="toctree-l2 current active has-children"><a class="current reference internal" href="#">Figure 3\n\nAnalysis and results for Figure 3.</a><details open="open"><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
+<li class="toctree-l2 current active has-children"><a class="current reference internal" href="#">Figure 3</a><details open="open"><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
 <li class="toctree-l3"><a class="reference internal" href="Figure_3a.html">Figure 3a. Colocalization patterns across three different molecular trait modalities (expression, splicing, protein abundance).</a></li>
 <li class="toctree-l3"><a class="reference internal" href="Figure_3b.html">Figure 3b. Distribution of the number of 95% CoSs corresponding to the different numbers of colocalized traits per locus.</a></li>
 
@@ -198,19 +198,19 @@
 <li class="toctree-l3"><a class="reference internal" href="Figure_3i.html">Figure 3i. Shared cell-types in primary CoS and secondary CoS.</a></li>
 </ul>
 </details></li>
-<li class="toctree-l2 has-children"><a class="reference internal" href="../Figure_4/index.html">Figure 4\n\nAnalysis and results for Figure 4.</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
+<li class="toctree-l2 has-children"><a class="reference internal" href="../Figure_4/index.html">Figure 4</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
 <li class="toctree-l3"><a class="reference internal" href="../Figure_4/Figure_4a.html">Figure 4a. Variant set -level Excess-of-overlap (EOO) analysis.</a></li>
 <li class="toctree-l3"><a class="reference internal" href="../Figure_4/Figure_4b.html">Figure 4b. Variant set -level Excess-of-overlap (EOO) analysis in bulk region.</a></li>
 <li class="toctree-l3"><a class="reference internal" href="../Figure_4/Figure_4c.html">Figure 4c. Variant set -level Excess-of-overlap (EOO) analysis in cell types.</a></li>
 <li class="toctree-l3"><a class="reference internal" href="../Figure_4/Figure_4d.html">Figure 4d. Microglia-specific eQTL colocalization in FCGR2A.</a></li>
 </ul>
 </details></li>
-<li class="toctree-l2 has-children"><a class="reference internal" href="../Figure_5/index.html">Figure 5\n\nAnalysis and results for Figure 5.</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
+<li class="toctree-l2 has-children"><a class="reference internal" href="../Figure_5/index.html">Figure 5</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
 <li class="toctree-l3"><a class="reference internal" href="../Figure_5/Figure_5abc.html">Figure 5abc. Disease heritability analyses of variant-level functional annotations derived from ColocBoost.</a></li>
 <li class="toctree-l3"><a class="reference internal" href="../Figure_5/Figure_5d.html">Figure 5d. Standardized effect sizes of the MaxVCP-xQTL and an analogous score based on the HyPrColoc method.</a></li>
 </ul>
 </details></li>
-<li class="toctree-l2 has-children"><a class="reference internal" href="../Figure_6/index.html">Figure 6\n\nAnalysis and results for Figure 6.</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
+<li class="toctree-l2 has-children"><a class="reference internal" href="../Figure_6/index.html">Figure 6</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
 <li class="toctree-l3"><a class="reference internal" href="../Figure_6/Figure_6a.html">Figure 6a. UpSet plot comparison.</a></li>
 <li class="toctree-l3"><a class="reference internal" href="../Figure_6/Figure_6b.html">Figure 6b. Scatter plot across variants in terms of the magnitude of quantile-matched z-scores.</a></li>
 <li class="toctree-l3"><a class="reference internal" href="../Figure_6/Figure_6c.html">Figure 6c. Distribution of distances from the gene TSS for CoS.</a></li>
@@ -405,7 +405,7 @@
 
 
 <div id="jb-print-docs-body" class="onlyprint">
-    <h1>Figure 3\n\nAnalysis and results for Figure 3.</h1>
+    <h1>Figure 3</h1>
     <!-- Table of contents -->
     <div id="print-main-content">
         <div id="jb-print-toc">
@@ -419,8 +419,9 @@ <h1>Figure 3\n\nAnalysis and results for Figure 3.</h1>
 <div id="searchbox"></div>
                 <article class="bd-article">
 
-  <section class="tex2jax_ignore mathjax_ignore" id="figure-3-n-nanalysis-and-results-for-figure-3">
-<h1>Figure 3\n\nAnalysis and results for Figure 3.<a class="headerlink" href="#figure-3-n-nanalysis-and-results-for-figure-3" title="Link to this heading">#</a></h1>
+  <section class="tex2jax_ignore mathjax_ignore" id="figure-3">
+<h1>Figure 3<a class="headerlink" href="#figure-3" title="Link to this heading">#</a></h1>
+<p>Analysis and results for Figure 3.</p>
 <div class="toctree-wrapper compound">
 </div>
 </section>