<!DOCTYPE html> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <meta charset="utf-8" /> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> <meta name="generator" content="pandoc" /> <title>CAUSE: Causal Analysis Using Summary Statistics</title> <script src="site_libs/jquery-1.11.3/jquery.min.js"></script> <meta name="viewport" content="width=device-width, initial-scale=1" /> <link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" /> <script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script> <script src="site_libs/bootstrap-3.3.5/shim/html5shiv.min.js"></script> <script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script> <script src="site_libs/navigation-1.1/tabsets.js"></script> <link href="site_libs/highlightjs-9.12.0/textmate.css" rel="stylesheet" /> <script src="site_libs/highlightjs-9.12.0/highlight.js"></script> <link href="site_libs/font-awesome-5.0.13/css/fa-svg-with-js.css" rel="stylesheet" /> <script src="site_libs/font-awesome-5.0.13/js/fontawesome-all.min.js"></script> <script src="site_libs/font-awesome-5.0.13/js/fa-v4-shims.min.js"></script> <style type="text/css">code{white-space: pre;}</style> <style type="text/css"> pre:not([class]) { background-color: white; } </style> <script type="text/javascript"> if (window.hljs) { hljs.configure({languages: []}); hljs.initHighlightingOnLoad(); if (document.readyState && document.readyState === "complete") { window.setTimeout(function() { hljs.initHighlighting(); }, 0); } } </script> <style type="text/css"> h1 { font-size: 34px; } h1.title { font-size: 38px; } h2 { font-size: 30px; } h3 { font-size: 24px; } h4 { font-size: 18px; } h5 { font-size: 16px; } h6 { font-size: 12px; } .table th:not([align]) { text-align: left; } </style> </head> <body> <style type = "text/css"> .main-container { max-width: 940px; margin-left: auto; margin-right: auto; } code { color: inherit; background-color: rgba(0, 0, 0, 0.04); } img { max-width:100%; height: auto; } .tabbed-pane { padding-top: 12px; } .html-widget { margin-bottom: 20px; } button.code-folding-btn:focus { outline: none; } </style> <style type="text/css"> /* padding for bootstrap navbar */ body { padding-top: 51px; padding-bottom: 40px; } /* offset scroll position for anchor links (for fixed navbar) */ .section h1 { padding-top: 56px; margin-top: -56px; } .section h2 { padding-top: 56px; margin-top: -56px; } .section h3 { padding-top: 56px; margin-top: -56px; } .section h4 { padding-top: 56px; margin-top: -56px; } .section h5 { padding-top: 56px; margin-top: -56px; } .section h6 { padding-top: 56px; margin-top: -56px; } </style> <script> // manage active state of menu based on current page $(document).ready(function () { // active menu anchor href = window.location.pathname href = href.substr(href.lastIndexOf('/') + 1) if (href === "") href = "index.html"; var menuAnchor = $('a[href="' + href + '"]'); // mark it active menuAnchor.parent().addClass('active'); // if it's got a parent navbar menu mark it active as well menuAnchor.closest('li.dropdown').addClass('active'); }); </script> <div class="container-fluid main-container"> <!-- tabsets --> <script> $(document).ready(function () { window.buildTabsets("TOC"); }); </script> <!-- code folding --> <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> <span class="icon-bar"></span> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> <a class="navbar-brand" href="index.html">CAUSE: Cauasl Analysis Using Summary Effects</a> </div> <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> <a href="index.html">Home</a> </li> <li> <a href="ldl_cad.html">R Package Tutorial</a> </li> <li> <a href="simulations.html">Simulations</a> </li> <li> <a href="gwas_pairs.html">Analyze Pairs of GWAS Traits</a> </li> <li> <a href="license.html">License</a> </li> </ul> <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jdblischak/workflowr"> <span class="fa fa-github"></span> </a> </li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> <!-- Add a small amount of space between sections. --> <style type="text/css"> div.section { padding-top: 12px; } </style> <div class="fluid-row" id="header"> <h1 class="title toc-ignore">CAUSE: Causal Analysis Using Summary Statistics</h1> </div> <p><strong>Last updated:</strong> 2019-06-25</p> <strong>workflowr checks:</strong> <small>(Click a bullet for more information)</small> <ul> <li> <p><details> <summary> <strong style="color:blue;">✔</strong> <strong>R Markdown file:</strong> up-to-date </summary></p> <p>Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.</p> </details> </li> <li> <p><details> <summary> <strong style="color:blue;">✔</strong> <strong>Repository version:</strong> <a href="https://github.com/jean997/cause/tree/a54a556ff8ac53d476f804f26088ddf95a9faac0" target="_blank">a54a556</a> </summary></p> Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility. The version displayed above was the version of the Git repository at the time these results were generated. <br><br> Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use <code>wflow_publish</code> or <code>wflow_git_commit</code>). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated: <pre><code> Ignored files: Ignored: .Rhistory Ignored: .Rproj.user/ Untracked files: Untracked: analysis/figure/ Untracked: analysis/ldl_cad_cache/ Untracked: example_data/CAD_META.gz Untracked: example_data/genome_wide_pruned_vars.1.RDS Untracked: example_data/glg_ldl__vanderHarst_cad_cause.RDS Untracked: example_data/glg_ldl__vanderHarst_cad_data.RDS Untracked: example_data/glg_ldl__vanderHarst_cad_grid.RDS Untracked: example_data/jointGwasMc_LDL.txt.gz Untracked: example_data/ld_data.tar.gz Untracked: example_data/ld_data/ Untracked: example_data/ldl_cad_cause.RDS Untracked: example_data/ldl_cad_cause.old_grid.RDS Untracked: example_data/ldl_cad_params.RDS Untracked: example_data/snp_overlap.txt Untracked: example_data/snp_overlap_ldpruned.txt Untracked: example_data/top_ldl_pruned_vars.1.RDS Untracked: ll_v7_notes.Rmd Untracked: matrix_lik.RDS Untracked: quantile_sampling.R Untracked: simulations/ Untracked: src/RcppExports.o Untracked: src/log_likelihood_functions.o Untracked: test_data/ </code></pre> Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes. </details> </li> </ul> <details> <summary> <small><strong>Expand here to see past versions:</strong></small> </summary> <ul> <table style="border-collapse:separate; border-spacing:5px;"> <thead> <tr> <th style="text-align:left;"> File </th> <th style="text-align:left;"> Version </th> <th style="text-align:left;"> Author </th> <th style="text-align:left;"> Date </th> <th style="text-align:left;"> Message </th> </tr> </thead> <tbody> <tr> <td style="text-align:left;"> Rmd </td> <td style="text-align:left;"> <a href="https://github.com/jean997/cause/blob/a54a556ff8ac53d476f804f26088ddf95a9faac0/analysis/index.Rmd" target="_blank">a54a556</a> </td> <td style="text-align:left;"> Jean Morrison </td> <td style="text-align:left;"> 2019-06-25 </td> <td style="text-align:left;"> wflow_publish(files = c(“analysis/index.Rmd”)) </td> </tr> <tr> <td style="text-align:left;"> html </td> <td style="text-align:left;"> <a href="https://cdn.rawgit.com/jean997/cause/6b826d9bdb72220b0de8c9723f892ba31d7ddf0b/docs/index.html" target="_blank">6b826d9</a> </td> <td style="text-align:left;"> Jean Morrison </td> <td style="text-align:left;"> 2019-06-25 </td> <td style="text-align:left;"> Build site. </td> </tr> <tr> <td style="text-align:left;"> html </td> <td style="text-align:left;"> <a href="https://cdn.rawgit.com/jean997/cause/286f4e9e0a432565b96c38bba3a1b155c02f9a78/docs/index.html" target="_blank">286f4e9</a> </td> <td style="text-align:left;"> Jean Morrison </td> <td style="text-align:left;"> 2019-06-25 </td> <td style="text-align:left;"> Build site. </td> </tr> <tr> <td style="text-align:left;"> Rmd </td> <td style="text-align:left;"> <a href="https://github.com/jean997/cause/blob/8f3b82e734b124b6d4d9d28b9defcce8d3726410/analysis/index.Rmd" target="_blank">8f3b82e</a> </td> <td style="text-align:left;"> Jean Morrison </td> <td style="text-align:left;"> 2019-06-25 </td> <td style="text-align:left;"> wflow_publish(files = c(“analysis/about.Rmd”, “analysis/index.Rmd”, “analysis/ldl_cad.Rmd”, “analysis/license.Rmd”, </td> </tr> <tr> <td style="text-align:left;"> html </td> <td style="text-align:left;"> <a href="https://cdn.rawgit.com/jean997/cause/46b159a1f6313e26149b7fb021b2d18aaf4bbd5c/docs/index.html" target="_blank">46b159a</a> </td> <td style="text-align:left;"> Jean Morrison </td> <td style="text-align:left;"> 2018-10-17 </td> <td style="text-align:left;"> Build site. </td> </tr> <tr> <td style="text-align:left;"> Rmd </td> <td style="text-align:left;"> <a href="https://github.com/jean997/cause/blob/19edfa41426350036d7812260cbdba1ca9a7bcda/analysis/index.Rmd" target="_blank">19edfa4</a> </td> <td style="text-align:left;"> Jean Morrison </td> <td style="text-align:left;"> 2018-10-17 </td> <td style="text-align:left;"> wflow_git_commit(“analysis/index.Rmd”) </td> </tr> <tr> <td style="text-align:left;"> html </td> <td style="text-align:left;"> <a href="https://cdn.rawgit.com/jean997/cause/f15238b6e5b2e1f07f8846e5c56618a8ba28b62a/docs/index.html" target="_blank">f15238b</a> </td> <td style="text-align:left;"> Jean Morrison </td> <td style="text-align:left;"> 2018-10-14 </td> <td style="text-align:left;"> Build site. </td> </tr> <tr> <td style="text-align:left;"> Rmd </td> <td style="text-align:left;"> <a href="https://github.com/jean997/cause/blob/d163752b8091f97bcf76e4b6b012a2f23954bfd8/analysis/index.Rmd" target="_blank">d163752</a> </td> <td style="text-align:left;"> Jean Morrison </td> <td style="text-align:left;"> 2018-10-14 </td> <td style="text-align:left;"> update about and index </td> </tr> <tr> <td style="text-align:left;"> Rmd </td> <td style="text-align:left;"> <a href="https://github.com/jean997/cause/blob/efc43ef89c766d22c038de5cb2b980fd1a7402c2/analysis/index.Rmd" target="_blank">efc43ef</a> </td> <td style="text-align:left;"> Jean Morrison </td> <td style="text-align:left;"> 2018-10-14 </td> <td style="text-align:left;"> Start workflowr project. </td> </tr> </tbody> </table> </ul> <p></details></p> <hr /> <p>Weclome to the CAUSE website!</p> <p><a href="url%20coming">Pre-print</a> <a href="https://github.com/jean997/cause">R package</a></p> <p>CAUSE is a Mendelian Randomization method using genome-wide summary statistics. CAUSE models both horizontal and correlated pleiotropy in order to avoid false positives that can occur using other methods.</p> <p>In this website you will find:</p> <ul> <li>A tutorial on how to use the cause R package</li> <li>Instructions for replicating simulations in the paper</li> <li>Instructions for replicating data analysis in the paper (coming soon)</li> </ul> <!-- Adjust MathJax settings so that all math formulae are shown using TeX fonts only; see http://docs.mathjax.org/en/latest/configuration.html. This will make the presentation more consistent at the cost of the webpage sometimes taking slightly longer to load. 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