<!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" /> <meta name="author" content="Lei Sun" /> <meta name="date" content="2018-04-03" /> <title>Variability of Knockoff’s FDR Control</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/readable.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/jqueryui-1.11.4/jquery-ui.min.js"></script> <link href="site_libs/tocify-1.9.1/jquery.tocify.css" rel="stylesheet" /> <script src="site_libs/tocify-1.9.1/jquery.tocify.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-4.5.0/css/font-awesome.min.css" rel="stylesheet" /> <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; } 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 --> <script> $(document).ready(function () { // move toc-ignore selectors from section div to header $('div.section.toc-ignore') .removeClass('toc-ignore') .children('h1,h2,h3,h4,h5').addClass('toc-ignore'); // establish options var options = { selectors: "h1,h2,h3", theme: "bootstrap3", context: '.toc-content', hashGenerator: function (text) { return text.replace(/[.\\/?&!#<>]/g, '').replace(/\s/g, '_').toLowerCase(); }, ignoreSelector: ".toc-ignore", scrollTo: 0 }; options.showAndHide = true; options.smoothScroll = true; // tocify var toc = $("#TOC").tocify(options).data("toc-tocify"); }); </script> <style type="text/css"> #TOC { margin: 25px 0px 20px 0px; } @media (max-width: 768px) { #TOC { position: relative; width: 100%; } } .toc-content { padding-left: 30px; padding-right: 40px; } div.main-container { max-width: 1200px; } div.tocify { width: 20%; max-width: 260px; max-height: 85%; } @media (min-width: 768px) and (max-width: 991px) { div.tocify { width: 25%; } } @media (max-width: 767px) { div.tocify { width: 100%; max-width: none; } } .tocify ul, .tocify li { line-height: 20px; } .tocify-subheader .tocify-item { font-size: 0.90em; padding-left: 25px; text-indent: 0; } .tocify .list-group-item { border-radius: 0px; } </style> <!-- setup 3col/9col grid for toc_float and main content --> <div class="row-fluid"> <div class="col-xs-12 col-sm-4 col-md-3"> <div id="TOC" class="tocify"> </div> </div> <div class="toc-content col-xs-12 col-sm-8 col-md-9"> <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">truncash</a> </div> <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> <a href="about.html">About</a> </li> <li> <a href="license.html">License</a> </li> </ul> <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/LSun/truncash"> <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">Variability of <code>Knockoff</code>’s FDR Control</h1> <h4 class="author"><em>Lei Sun</em></h4> <h4 class="date"><em>2018-04-03</em></h4> </div> <p><strong>Last updated:</strong> 2018-05-15</p> <strong>workflowr checks:</strong> <small>(Click a bullet for more information)</small> <ul> <li> <details> <p><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> <details> <p><summary> <strong style="color:blue;">✔</strong> <strong>Environment:</strong> empty </summary></p> <p>Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.</p> </details> </li> <li> <details> <p><summary> <strong style="color:blue;">✔</strong> <strong>Seed:</strong> <code>set.seed(12345)</code> </summary></p> <p>The command <code>set.seed(12345)</code> was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.</p> </details> </li> <li> <details> <p><summary> <strong style="color:blue;">✔</strong> <strong>Session information:</strong> recorded </summary></p> <p>Great job! Recording the operating system, R version, and package versions is critical for reproducibility.</p> </details> </li> <li> <details> <p><summary> <strong style="color:blue;">✔</strong> <strong>Repository version:</strong> <a href="https://github.com/LSun/truncash/tree/388e65e06000e313c170a82f3ed57346f6024897" target="_blank">388e65e</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: .DS_Store Ignored: .Rhistory Ignored: .Rproj.user/ Ignored: analysis/.DS_Store Ignored: analysis/BH_robustness_cache/ Ignored: analysis/FDR_Null_cache/ Ignored: analysis/FDR_null_betahat_cache/ Ignored: analysis/Rmosek_cache/ Ignored: analysis/StepDown_cache/ Ignored: analysis/alternative2_cache/ Ignored: analysis/alternative_cache/ Ignored: analysis/ash_gd_cache/ Ignored: analysis/average_cor_gtex_2_cache/ Ignored: analysis/average_cor_gtex_cache/ Ignored: analysis/brca_cache/ Ignored: analysis/cash_deconv_cache/ Ignored: analysis/cash_fdr_1_cache/ Ignored: analysis/cash_fdr_2_cache/ Ignored: analysis/cash_fdr_3_cache/ Ignored: analysis/cash_fdr_4_cache/ Ignored: analysis/cash_fdr_5_cache/ Ignored: analysis/cash_fdr_6_cache/ Ignored: analysis/cash_plots_cache/ Ignored: analysis/cash_sim_1_cache/ Ignored: analysis/cash_sim_2_cache/ Ignored: analysis/cash_sim_3_cache/ Ignored: analysis/cash_sim_4_cache/ Ignored: analysis/cash_sim_5_cache/ Ignored: analysis/cash_sim_6_cache/ Ignored: analysis/cash_sim_7_cache/ Ignored: analysis/correlated_z_2_cache/ Ignored: analysis/correlated_z_3_cache/ Ignored: analysis/correlated_z_cache/ Ignored: analysis/create_null_cache/ Ignored: analysis/cutoff_null_cache/ Ignored: analysis/design_matrix_2_cache/ Ignored: analysis/design_matrix_cache/ Ignored: analysis/diagnostic_ash_cache/ Ignored: analysis/diagnostic_correlated_z_2_cache/ Ignored: analysis/diagnostic_correlated_z_3_cache/ Ignored: analysis/diagnostic_correlated_z_cache/ Ignored: analysis/diagnostic_plot_2_cache/ Ignored: analysis/diagnostic_plot_cache/ Ignored: analysis/efron_leukemia_cache/ Ignored: analysis/fitting_normal_cache/ Ignored: analysis/gaussian_derivatives_2_cache/ Ignored: analysis/gaussian_derivatives_3_cache/ Ignored: analysis/gaussian_derivatives_4_cache/ Ignored: analysis/gaussian_derivatives_5_cache/ Ignored: analysis/gaussian_derivatives_cache/ Ignored: analysis/gd-ash_cache/ Ignored: analysis/gd_delta_cache/ Ignored: analysis/gd_lik_2_cache/ Ignored: analysis/gd_lik_cache/ Ignored: analysis/gd_w_cache/ Ignored: analysis/knockoff_10_cache/ Ignored: analysis/knockoff_2_cache/ Ignored: analysis/knockoff_3_cache/ Ignored: analysis/knockoff_4_cache/ Ignored: analysis/knockoff_5_cache/ Ignored: analysis/knockoff_6_cache/ Ignored: analysis/knockoff_7_cache/ Ignored: analysis/knockoff_8_cache/ Ignored: analysis/knockoff_9_cache/ Ignored: analysis/knockoff_cache/ Ignored: analysis/knockoff_var_cache/ Ignored: analysis/marginal_z_alternative_cache/ Ignored: analysis/marginal_z_cache/ Ignored: analysis/mosek_reg_2_cache/ Ignored: analysis/mosek_reg_4_cache/ Ignored: analysis/mosek_reg_5_cache/ Ignored: analysis/mosek_reg_6_cache/ Ignored: analysis/mosek_reg_cache/ Ignored: analysis/pihat0_null_cache/ Ignored: analysis/plot_diagnostic_cache/ Ignored: analysis/poster_obayes17_cache/ Ignored: analysis/real_data_simulation_2_cache/ Ignored: analysis/real_data_simulation_3_cache/ Ignored: analysis/real_data_simulation_4_cache/ Ignored: analysis/real_data_simulation_5_cache/ Ignored: analysis/real_data_simulation_cache/ Ignored: analysis/rmosek_primal_dual_2_cache/ Ignored: analysis/rmosek_primal_dual_cache/ Ignored: analysis/seqgendiff_cache/ Ignored: analysis/simulated_correlated_null_2_cache/ Ignored: analysis/simulated_correlated_null_3_cache/ Ignored: analysis/simulated_correlated_null_cache/ Ignored: analysis/simulation_real_se_2_cache/ Ignored: analysis/simulation_real_se_cache/ Ignored: analysis/smemo_2_cache/ Ignored: data/LSI/ Ignored: docs/.DS_Store Ignored: docs/figure/.DS_Store Ignored: output/fig/ </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;"> html </td> <td style="text-align:left;"> <a href="https://cdn.rawgit.com/LSun/truncash/e05bc836b3c74dc6ebca415afb5938675d6c5436/docs/knockoff_var.html" target="_blank">e05bc83</a> </td> <td style="text-align:left;"> LSun </td> <td style="text-align:left;"> 2018-05-12 </td> <td style="text-align:left;"> Update to 1.0 </td> </tr> <tr> <td style="text-align:left;"> rmd </td> <td style="text-align:left;"> <a href="https://github.com/LSun/truncash/blob/cc0ab8379469bc3726f1508cd81e4ecd6fef1b1a/analysis/knockoff_var.rmd" target="_blank">cc0ab83</a> </td> <td style="text-align:left;"> Lei Sun </td> <td style="text-align:left;"> 2018-05-11 </td> <td style="text-align:left;"> update </td> </tr> <tr> <td style="text-align:left;"> html </td> <td style="text-align:left;"> <a href="https://cdn.rawgit.com/LSun/truncash/21e639d9fabe7fb1e54a45ab6bd470a68097924a/docs/knockoff_var.html" target="_blank">21e639d</a> </td> <td style="text-align:left;"> LSun </td> <td style="text-align:left;"> 2018-04-05 </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/LSun/truncash/blob/11873994c6fefccbc7aecc7bce9c32671ee6ccba/analysis/knockoff_var.rmd" target="_blank">1187399</a> </td> <td style="text-align:left;"> LSun </td> <td style="text-align:left;"> 2018-04-05 </td> <td style="text-align:left;"> wflow_publish(“analysis/knockoff_var.rmd”) </td> </tr> <tr> <td style="text-align:left;"> rmd </td> <td style="text-align:left;"> <a href="https://github.com/LSun/truncash/blob/69aab5a63653609d4dcdb364bfa7be66f67cff20/analysis/knockoff_var.rmd" target="_blank">69aab5a</a> </td> <td style="text-align:left;"> Lei Sun </td> <td style="text-align:left;"> 2018-04-03 </td> <td style="text-align:left;"> knockoff variability </td> </tr> <tr> <td style="text-align:left;"> html </td> <td style="text-align:left;"> <a href="https://cdn.rawgit.com/LSun/truncash/6af9b53bf86bc43dabecc0173cbb79c2b98626a4/docs/knockoff_var.html" target="_blank">6af9b53</a> </td> <td style="text-align:left;"> LSun </td> <td style="text-align:left;"> 2018-04-03 </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/LSun/truncash/blob/5bce84a27c3f19aeac398409c9a2ed86ff8c0033/analysis/knockoff_var.rmd" target="_blank">5bce84a</a> </td> <td style="text-align:left;"> LSun </td> <td style="text-align:left;"> 2018-04-03 </td> <td style="text-align:left;"> wflow_publish(c(“knockoff_6.rmd”, “knockoff_var.rmd”)) </td> </tr> </tbody> </table> </ul> </details> <hr /> <div id="introduction" class="section level2"> <h2>Introduction</h2> <p>We hypothesize that <code>Knockoff</code> might have a potential problem: the variability of the actual FDP could be large, although the mean of FDP is theoretically and empirically controlled at FDR.</p> <p>The reason is that <code>Knockoff</code> relies on the <strong>flip sign property</strong> of the test statistics <span class="math inline">\(W_j\)</span> for all null variables. Actually the events <span class="math inline">\(\{W_j \geq t_j\}\)</span> or <span class="math inline">\(\{W_j \leq -t_j\}\)</span> are independent for all null variables. However, they are <strong>not identically distributed</strong>.</p> <p>Therefore, if every null variable is “unique,” in the sense that its test statistic has a distinct distribution, for example, if it tends to be larger or in a different region than anyone else, then this test statistic could randomly be positive or negative, and affect the estimate of FDP for different random samples.</p> <p>In common high-dimensional settings it’s usually not a big problem since in those simulations no null variables are unique, meaning that we would expect to see <span class="math inline">\(W_i\)</span> and <span class="math inline">\(W_j\)</span> showing up in regions symmetric at zero.</p> </div> <div id="a-simple-illustration" class="section level2"> <h2>A simple illustration</h2> <p><span class="math inline">\(X\)</span> is <span class="math inline">\(30 \times 4\)</span>, <span class="math inline">\(X_1\)</span> and <span class="math inline">\(X_3\)</span> are “true” variables, and <span class="math inline">\(X_2\)</span> and <span class="math inline">\(X_4\)</span> are nulls. <span class="math inline">\(X_2\)</span> is highly correlated with <span class="math inline">\(X_1\)</span>, <span class="math inline">\(\rho = 0.99\)</span>, whereas <span class="math inline">\(X_4\)</span> is almost uncorrelated with <span class="math inline">\(X_3\)</span>, <span class="math inline">\(\rho = 0.01\)</span>.</p> <p>Below is a plot of <span class="math inline">\(W_2\)</span> vs <span class="math inline">\(W_4\)</span>. As we can see, <span class="math inline">\(|W_2|\)</span> is usually much greater than <span class="math inline">\(|W_4|\)</span>, and in many samples, only <span class="math inline">\(W_2\)</span> will show up in the rejection region <span class="math inline">\(W \geq t\)</span> or its symmetric null estimation region <span class="math inline">\(W \le -t\)</span>, which brings variability of <span class="math inline">\(\hat{FDP}\)</span> as the null statistic <span class="math inline">\(W_2\)</span> shows up in one region or the other.</p> <p><img src="figure/knockoff_var.rmd/simple_var-1.png" width="672" style="display: block; margin: auto;" /></p> </div> <div id="example" class="section level2"> <h2>Example</h2> <p><span class="math inline">\(X\)</span> is <span class="math inline">\(n \times 20\)</span>. There are <span class="math inline">\(10\)</span> “true” variables: <span class="math inline">\(X_1, X_3, X_5, \ldots, X_{17}, X_{19}\)</span> and <span class="math inline">\(10\)</span> null variables: <span class="math inline">\(X_2, X_4, X_6, \ldots, X_{18}, X_{20}\)</span>. The correlation between the true and null variables are decreasing such that <span class="math inline">\(\rho(X_1, X_2) = 0.9, \rho(X_3, X_4) = 0.8, \rho(X_5, X_6) = 0.7, \ldots, \rho(X_{17}, X_{18}) = 0.2, \rho(X_{19}, X_{20}) = 0.1\)</span>, and all other pairwise correlations are zero.</p> <div id="n-30" class="section level3"> <h3><span class="math inline">\(n = 30\)</span></h3> <p>The variability in FDP given by <code>Knockoff</code> is obvious.</p> <p><img src="figure/knockoff_var.rmd/unnamed-chunk-4-1.png" width="672" style="display: block; margin: auto;" /></p> <details> <summary><em>Expand here to see past versions of unnamed-chunk-4-1.png:</em></summary> <table style = "border-collapse:separate; border-spacing:5px;"> <thead> <tr> <th style="text-align:left;"> Version </th> <th style="text-align:left;"> Author </th> <th style="text-align:left;"> Date </th> </tr> </thead> <tbody> <tr> <td style="text-align:left;"> <a href="https://github.com/LSun/truncash/blob/21e639d9fabe7fb1e54a45ab6bd470a68097924a/docs/figure/knockoff_var.rmd/unnamed-chunk-4-1.png" target="_blank">21e639d</a> </td> <td style="text-align:left;"> LSun </td> <td style="text-align:left;"> 2018-04-05 </td> </tr> </tbody> </table> </details> <p><img src="figure/knockoff_var.rmd/unnamed-chunk-4-2.png" width="672" style="display: block; margin: auto;" /></p> <details> <summary><em>Expand here to see past versions of unnamed-chunk-4-2.png:</em></summary> <table style = "border-collapse:separate; border-spacing:5px;"> <thead> <tr> <th style="text-align:left;"> Version </th> <th style="text-align:left;"> Author </th> <th style="text-align:left;"> Date </th> </tr> </thead> <tbody> <tr> <td style="text-align:left;"> <a href="https://github.com/LSun/truncash/blob/21e639d9fabe7fb1e54a45ab6bd470a68097924a/docs/figure/knockoff_var.rmd/unnamed-chunk-4-2.png" target="_blank">21e639d</a> </td> <td style="text-align:left;"> LSun </td> <td style="text-align:left;"> 2018-04-05 </td> </tr> </tbody> </table> </details> <p><img src="figure/knockoff_var.rmd/unnamed-chunk-4-3.png" width="672" style="display: block; margin: auto;" /></p> <details> <summary><em>Expand here to see past versions of unnamed-chunk-4-3.png:</em></summary> <table style = "border-collapse:separate; border-spacing:5px;"> <thead> <tr> <th style="text-align:left;"> Version </th> <th style="text-align:left;"> Author </th> <th style="text-align:left;"> Date </th> </tr> </thead> <tbody> <tr> <td style="text-align:left;"> <a href="https://github.com/LSun/truncash/blob/21e639d9fabe7fb1e54a45ab6bd470a68097924a/docs/figure/knockoff_var.rmd/unnamed-chunk-4-3.png" target="_blank">21e639d</a> </td> <td style="text-align:left;"> LSun </td> <td style="text-align:left;"> 2018-04-05 </td> </tr> </tbody> </table> </details> <p><img src="figure/knockoff_var.rmd/unnamed-chunk-4-4.png" width="672" style="display: block; margin: auto;" /></p> <details> <summary><em>Expand here to see past versions of unnamed-chunk-4-4.png:</em></summary> <table style = "border-collapse:separate; border-spacing:5px;"> <thead> <tr> <th style="text-align:left;"> Version </th> <th style="text-align:left;"> Author </th> <th style="text-align:left;"> Date </th> </tr> </thead> <tbody> <tr> <td style="text-align:left;"> <a href="https://github.com/LSun/truncash/blob/21e639d9fabe7fb1e54a45ab6bd470a68097924a/docs/figure/knockoff_var.rmd/unnamed-chunk-4-4.png" target="_blank">21e639d</a> </td> <td style="text-align:left;"> LSun </td> <td style="text-align:left;"> 2018-04-05 </td> </tr> </tbody> </table> </details> </div> <div id="n-10k" class="section level3"> <h3><span class="math inline">\(n = 10K\)</span></h3> <p>The variability in FDP given by <code>Knockoff</code> is less than when <span class="math inline">\(n = 30\)</span>, but still bigger than that given by <code>BH</code>.</p> <p><img src="figure/knockoff_var.rmd/unnamed-chunk-5-1.png" width="672" style="display: block; margin: auto;" /></p> <details> <summary><em>Expand here to see past versions of unnamed-chunk-5-1.png:</em></summary> <table style = "border-collapse:separate; border-spacing:5px;"> <thead> <tr> <th style="text-align:left;"> Version </th> <th style="text-align:left;"> Author </th> <th style="text-align:left;"> Date </th> </tr> </thead> <tbody> <tr> <td style="text-align:left;"> <a href="https://github.com/LSun/truncash/blob/21e639d9fabe7fb1e54a45ab6bd470a68097924a/docs/figure/knockoff_var.rmd/unnamed-chunk-5-1.png" target="_blank">21e639d</a> </td> <td style="text-align:left;"> LSun </td> <td style="text-align:left;"> 2018-04-05 </td> </tr> </tbody> </table> </details> <p><img src="figure/knockoff_var.rmd/unnamed-chunk-5-2.png" width="672" style="display: block; margin: auto;" /></p> <details> <summary><em>Expand here to see past versions of unnamed-chunk-5-2.png:</em></summary> <table style = "border-collapse:separate; border-spacing:5px;"> <thead> <tr> <th style="text-align:left;"> Version </th> <th style="text-align:left;"> Author </th> <th style="text-align:left;"> Date </th> </tr> </thead> <tbody> <tr> <td style="text-align:left;"> <a href="https://github.com/LSun/truncash/blob/21e639d9fabe7fb1e54a45ab6bd470a68097924a/docs/figure/knockoff_var.rmd/unnamed-chunk-5-2.png" target="_blank">21e639d</a> </td> <td style="text-align:left;"> LSun </td> <td style="text-align:left;"> 2018-04-05 </td> </tr> </tbody> </table> </details> <p><img src="figure/knockoff_var.rmd/unnamed-chunk-5-3.png" width="672" style="display: block; margin: auto;" /></p> <details> <summary><em>Expand here to see past versions of unnamed-chunk-5-3.png:</em></summary> <table style = "border-collapse:separate; border-spacing:5px;"> <thead> <tr> <th style="text-align:left;"> Version </th> <th style="text-align:left;"> Author </th> <th style="text-align:left;"> Date </th> </tr> </thead> <tbody> <tr> <td style="text-align:left;"> <a href="https://github.com/LSun/truncash/blob/21e639d9fabe7fb1e54a45ab6bd470a68097924a/docs/figure/knockoff_var.rmd/unnamed-chunk-5-3.png" target="_blank">21e639d</a> </td> <td style="text-align:left;"> LSun </td> <td style="text-align:left;"> 2018-04-05 </td> </tr> </tbody> </table> </details> <p><img src="figure/knockoff_var.rmd/unnamed-chunk-5-4.png" width="672" style="display: block; margin: auto;" /></p> <details> <summary><em>Expand here to see past versions of unnamed-chunk-5-4.png:</em></summary> <table style = "border-collapse:separate; border-spacing:5px;"> <thead> <tr> <th style="text-align:left;"> Version </th> <th style="text-align:left;"> Author </th> <th style="text-align:left;"> Date </th> </tr> </thead> <tbody> <tr> <td style="text-align:left;"> <a href="https://github.com/LSun/truncash/blob/21e639d9fabe7fb1e54a45ab6bd470a68097924a/docs/figure/knockoff_var.rmd/unnamed-chunk-5-4.png" target="_blank">21e639d</a> </td> <td style="text-align:left;"> LSun </td> <td style="text-align:left;"> 2018-04-05 </td> </tr> </tbody> </table> </details> </div> </div> <div id="session-information" class="section level2"> <h2>Session information</h2> <pre class="r"><code>sessionInfo()</code></pre> <pre><code>R version 3.4.3 (2017-11-30) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS High Sierra 10.13.4 Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] forcats_0.2.0 stringr_1.3.0 dplyr_0.7.4 purrr_0.2.4 [5] readr_1.1.1 tidyr_0.7.2 tibble_1.4.1 ggplot2_2.2.1 [9] tidyverse_1.2.1 Matrix_1.2-12 knockoff_0.3.0 loaded via a namespace (and not attached): [1] reshape2_1.4.3 haven_1.1.0 lattice_0.20-35 [4] colorspace_1.3-2 htmltools_0.3.6 yaml_2.1.18 [7] rlang_0.1.6 R.oo_1.21.0 pillar_1.0.1 [10] foreign_0.8-69 glue_1.2.0 R.utils_2.6.0 [13] readxl_1.0.0 modelr_0.1.1 bindrcpp_0.2 [16] bindr_0.1 plyr_1.8.4 cellranger_1.1.0 [19] munsell_0.4.3 gtable_0.2.0 workflowr_1.0.1 [22] rvest_0.3.2 R.methodsS3_1.7.1 psych_1.7.8 [25] evaluate_0.10.1 labeling_0.3 knitr_1.20 [28] parallel_3.4.3 broom_0.4.3 Rcpp_0.12.16 [31] backports_1.1.2 scales_0.5.0 jsonlite_1.5 [34] mnormt_1.5-5 hms_0.4.0 digest_0.6.15 [37] stringi_1.1.6 grid_3.4.3 rprojroot_1.3-2 [40] cli_1.0.0 tools_3.4.3 magrittr_1.5 [43] lazyeval_0.2.1 crayon_1.3.4 whisker_0.3-2 [46] pkgconfig_2.0.1 xml2_1.1.1 lubridate_1.7.1 [49] rstudioapi_0.7 assertthat_0.2.0 rmarkdown_1.9 [52] httr_1.3.1 R6_2.2.2 nlme_3.1-131 [55] git2r_0.21.0 compiler_3.4.3 </code></pre> </div> <!-- 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. Note that this only works because the footer is added to webpages before the MathJax javascript. --> <script type="text/x-mathjax-config"> MathJax.Hub.Config({ "HTML-CSS": { availableFonts: ["TeX"] } }); </script> <hr> <p> This reproducible <a href="http://rmarkdown.rstudio.com">R Markdown</a> analysis was created with <a href="https://github.com/jdblischak/workflowr">workflowr</a> 1.0.1 </p> <hr> </div> </div> </div> <script> // add bootstrap table styles to pandoc tables function bootstrapStylePandocTables() { $('tr.header').parent('thead').parent('table').addClass('table table-condensed'); } $(document).ready(function () { bootstrapStylePandocTables(); }); </script> <!-- dynamically load mathjax for compatibility with self-contained --> <script> (function () { var script = document.createElement("script"); script.type = "text/javascript"; script.src = "https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"; document.getElementsByTagName("head")[0].appendChild(script); })(); </script> </body> </html>