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<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
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<title>License</title>
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<style type="text/css">code{white-space: pre;}</style>
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pre:not([class]) {
background-color: white;
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hljs.configure({languages: []});
hljs.initHighlightingOnLoad();
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window.setTimeout(function() { hljs.initHighlighting(); }, 0);
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</script>
<style type="text/css">
h1 {
font-size: 34px;
}
h1.title {
font-size: 38px;
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font-size: 30px;
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font-size: 12px;
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text-align: left;
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background-color: rgba(0, 0, 0, 0.04);
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margin-left: 10px;
border-radius: 6px 0 6px 6px;
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// manage active state of menu based on current page
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// mark it active
menuAnchor.parent().addClass('active');
// if it's got a parent navbar menu mark it active as well
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});
</script>
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display: inline-table;
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.tabset-dropdown > .nav-tabs.nav-tabs-open > li {
display: block;
float: none;
}
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display: none;
}
</style>
<script>
$(document).ready(function () {
window.buildTabsets("TOC");
});
$(document).ready(function () {
$('.tabset-dropdown > .nav-tabs > li').click(function () {
$(this).parent().toggleClass('nav-tabs-open')
});
});
</script>
<!-- code folding -->
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<h1 class="title toc-ignore">License</h1>
</div>
<p>
<button type="button" class="btn btn-default btn-workflowr btn-workflowr-report" data-toggle="collapse" data-target="#workflowr-report">
<span class="glyphicon glyphicon-list" aria-hidden="true"></span> workflowr <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span>
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<p>
<strong>Last updated:</strong> 2020-02-25
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<p>
<strong>Checks:</strong> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> 2 <span class="glyphicon glyphicon-exclamation-sign text-danger" aria-hidden="true"></span> 0
</p>
<p>
<strong>Knit directory:</strong> <code>csna_workflow/</code> <span class="glyphicon glyphicon-question-sign" aria-hidden="true" title="This is the local directory in which the code in this file was executed."> </span>
</p>
<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> (version 1.4.0). The <em>Checks</em> tab describes the reproducibility checks that were applied when the results were created. The <em>Past versions</em> tab lists the development history.
</p>
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<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongRMarkdownfilestronguptodate"> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> <strong>R Markdown file:</strong> up-to-date </a>
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<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>
</div>
</div>
</div>
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<div class="panel-heading">
<p class="panel-title">
<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongRepositoryversionstrongahrefhttpsgithubcomTheJacksonLaboratoryCSNAtree259f3a57773a79cddc8994915d7df19e6cdc7e8dtargetblank259f3a5a"> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> <strong>Repository version:</strong> <a href="https://github.com/TheJacksonLaboratory/CSNA/tree/259f3a57773a79cddc8994915d7df19e6cdc7e8d" target="_blank">259f3a5</a> </a>
</p>
</div>
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<div class="panel-body">
<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:
</p>
<pre><code>
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Unstaged changes:
Modified: README.md
Modified: _workflowr.yml
Modified: analysis/01_geneseek2qtl2.R
Modified: analysis/02_geneseek2intensity.R
Modified: analysis/03_firstgm2genoprobs.R
Modified: analysis/04_diagnosis_qc_gigamuga_nine_batches.R
Modified: analysis/06_final_pr_apr_69K.R
Modified: analysis/07.1_html_founder_prop.R
Modified: analysis/07_recomb_size_founder_prop.R
Modified: analysis/08_gcta_herit.R
Modified: analysis/09_qtlmapping.R
Modified: analysis/10_qtl_permu.R
Modified: analysis/11_qtl_blup.R
Modified: analysis/run_01_geneseek2qtl2.R
Modified: analysis/run_02_geneseek2intensity.R
Modified: analysis/run_03_firstgm2genoprobs.R
Modified: analysis/run_04_diagnosis_qc_gigamuga_nine_batches.R
Modified: analysis/run_05_after_diagnosis_qc_gigamuga_nine_batches.R
Modified: analysis/run_06_final_pr_apr_69K.R
Modified: analysis/run_07.1_html_founder_prop.R
Modified: analysis/run_07_recomb_size_founder_prop.R
Modified: analysis/run_08_gcta_herit.R
Modified: analysis/run_09_qtlmapping.R
Modified: analysis/run_10_qtl_permu.R
Modified: analysis/run_11_qtl_blup.R
</code></pre>
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