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<p><strong>Last updated:</strong> 2018-07-01</p>
<strong>workflowr checks:</strong> <small>(Click a bullet for more information)</small>
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<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>
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<details>
<p><summary> <strong style="color:blue;">✔</strong> <strong>Repository version:</strong> <a href="https://github.com/xiangzhu/rss-gsea/tree/07473ff4d2486e334e710d8b9e6af666ecd06ac6" target="_blank">07473ff</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:
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Ignored files:
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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.
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<summary> <small><strong>Expand here to see past versions:</strong></small> </summary>
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<a href="https://github.com/xiangzhu/rss-gsea/blob/07473ff4d2486e334e710d8b9e6af666ecd06ac6/analysis/index.Rmd" target="_blank">07473ff</a>
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Xiang Zhu
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2018-07-01
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<td style="text-align:left;">
Xiang Zhu
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<td style="text-align:left;">
2018-06-30
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Build site.
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<a href="https://github.com/xiangzhu/rss-gsea/blob/e364292a90d4fd54c9c956ca2fb3770b18d42c1d/analysis/index.Rmd" target="_blank">e364292</a>
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<td style="text-align:left;">
Xiang Zhu
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<td style="text-align:left;">
2018-06-30
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wflow_publish(“index.Rmd”)
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html
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<a href="https://cdn.rawgit.com/xiangzhu/rss-gsea/de49400e509e7d1db688fe94b52307210fe208a5/docs/index.html" target="_blank">de49400</a>
</td>
<td style="text-align:left;">
Xiang Zhu
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<td style="text-align:left;">
2018-06-29
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Build site.
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<td style="text-align:left;">
Xiang Zhu
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<td style="text-align:left;">
2018-06-29
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wflow_publish(“index.Rmd”)
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html
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</td>
<td style="text-align:left;">
Xiang Zhu
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<td style="text-align:left;">
2018-06-27
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Build site.
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<a href="https://github.com/xiangzhu/rss-gsea/blob/bc9746a9e817d6e677d5b256c8c759975d96229a/analysis/index.Rmd" target="_blank">bc9746a</a>
</td>
<td style="text-align:left;">
Xiang Zhu
</td>
<td style="text-align:left;">
2018-06-27
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wflow_publish(“index.Rmd”)
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html
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<a href="https://cdn.rawgit.com/xiangzhu/rss-gsea/c749ac73c66b895dc8f555a431e08160f17054db/docs/index.html" target="_blank">c749ac7</a>
</td>
<td style="text-align:left;">
Xiang Zhu
</td>
<td style="text-align:left;">
2018-06-27
</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/xiangzhu/rss-gsea/blob/6006659014276b35f67c330a718a6349cb82f7b6/analysis/index.Rmd" target="_blank">6006659</a>
</td>
<td style="text-align:left;">
Xiang Zhu
</td>
<td style="text-align:left;">
2018-06-27
</td>
<td style="text-align:left;">
wflow_publish(“index.Rmd”)
</td>
</tr>
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<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/xiangzhu/rss-gsea/0852676bda1f16f5333f8dc713f06ee17541bdaf/docs/index.html" target="_blank">0852676</a>
</td>
<td style="text-align:left;">
Xiang Zhu
</td>
<td style="text-align:left;">
2018-06-27
</td>
<td style="text-align:left;">
Build site.
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<td style="text-align:left;">
Rmd
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<a href="https://github.com/xiangzhu/rss-gsea/blob/46603f37950862f3be5fcfd49e01cbd6ad33f6d6/analysis/index.Rmd" target="_blank">46603f3</a>
</td>
<td style="text-align:left;">
Xiang Zhu
</td>
<td style="text-align:left;">
2018-06-27
</td>
<td style="text-align:left;">
wflow_publish(“index.Rmd”)
</td>
</tr>
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<td style="text-align:left;">
html
</td>
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<a href="https://cdn.rawgit.com/xiangzhu/rss-gsea/ff6afd099209881334e83a9ee89642acaa830a53/docs/index.html" target="_blank">ff6afd0</a>
</td>
<td style="text-align:left;">
Xiang Zhu
</td>
<td style="text-align:left;">
2018-06-26
</td>
<td style="text-align:left;">
Build site.
</td>
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<td style="text-align:left;">
Rmd
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<a href="https://github.com/xiangzhu/rss-gsea/blob/bf31edf7399b4528d58a2cc7700bcb79724d604b/analysis/index.Rmd" target="_blank">bf31edf</a>
</td>
<td style="text-align:left;">
Xiang Zhu
</td>
<td style="text-align:left;">
2018-06-26
</td>
<td style="text-align:left;">
wflow_publish(files = c(“analysis/index.Rmd”, “analysis/license.Rmd”))
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html
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<a href="https://cdn.rawgit.com/xiangzhu/rss-gsea/33aa5b386ec7c6975848c7418c9da30e3cfdef51/docs/index.html" target="_blank">33aa5b3</a>
</td>
<td style="text-align:left;">
Xiang Zhu
</td>
<td style="text-align:left;">
2018-06-26
</td>
<td style="text-align:left;">
Build site.
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Rmd
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<td style="text-align:left;">
<a href="https://github.com/xiangzhu/rss-gsea/blob/02b392f1f926e36540994949f178d074e464988e/analysis/index.Rmd" target="_blank">02b392f</a>
</td>
<td style="text-align:left;">
Xiang Zhu
</td>
<td style="text-align:left;">
2018-06-26
</td>
<td style="text-align:left;">
wflow_publish(“analysis/index.Rmd”)
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/xiangzhu/rss-gsea/blob/cee1a927d6f181bac1305b4fdd1fe984707b9346/analysis/index.Rmd" target="_blank">cee1a92</a>
</td>
<td style="text-align:left;">
Xiang Zhu
</td>
<td style="text-align:left;">
2018-06-26
</td>
<td style="text-align:left;">
Start workflowr project.
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</ul>
</details>
<hr />
<div id="overview" class="section level2">
<h2>Overview</h2>
<p>This is my online notebook to document and share the full results of genome-wide enrichment analyses described in the manuscript:</p>
<blockquote>
<p>Xiang Zhu and Matthew Stephens (2017). A large-scale genome-wide enrichment analysis identifies new trait-associated genes, pathways and tissues across 31 human phenotypes. <em>bioRxiv.</em> <a href="https://doi.org/10.1101/160770" class="uri">https://doi.org/10.1101/160770</a>.</p>
</blockquote>
<p>The software that was used to generate these results is available at <a href="https://github.com/stephenslab/rss/tree/master/src_vb" class="uri">https://github.com/stephenslab/rss/tree/master/src_vb</a>. Here is an <a href="http://stephenslab.github.io/rss/Example-5">example</a> illustrating how to use this software to perform genome-wide enrichment analyses of GWAS summary statistics.</p>
<p>If you find results shown in this notebook and/or methods implemented in the software useful for your work, please cite the manuscript listed above, <a href="https://doi.org/10.1101/160770">Zhu and Stephens (2017)</a>.</p>
<p>If you have any question about this notebook or the software, please feel free to contact me: <a href="https://github.com/xiangzhu">Xiang Zhu</a>, <code>xiangzhu@uchicago.edu</code> or <code>xiangzhu@stanford.edu</code>.</p>
</div>
<div id="results" class="section level2">
<h2>Results</h2>
<div id="anthropometric-phenotypes" class="section level4">
<h4>Anthropometric phenotypes</h4>
<ul>
<li><a href="height_2014.html">Adult human height (Wood et al. 2014)</a></li>
<li><a href="bmi_2015.html">Body mass index (Locke et al. 2015)</a></li>
<li><a href="waist_2015.html">Waist-to-hip ratio (Shungin et al. 2015)</a></li>
</ul>
</div>
<div id="hematopoietic-phenotypes" class="section level4">
<h4>Hematopoietic phenotypes</h4>
<ul>
<li><a href="rbc_2012.html">Red blood cell count (Harst et al. 2012)</a></li>
</ul>
</div>
<div id="immune-related-phenotypes" class="section level4">
<h4>Immune-related phenotypes</h4>
<ul>
<li>[Rheumatoid arthritis (Okada et al. 2014)][ra_2014.html]</li>
<li><a href="ibd_2015.html">Crohn’s disease (Liu et al. 2015)</a></li>
<li><a href="ibd_2015.html">Inflammatory bowel disease (Liu et al. 2015)</a></li>
<li><a href="ibd_2015.html">Ulcerative colitis (Liu et al. 2015)</a></li>
</ul>
</div>
<div id="metabolic-phenotypes" class="section level4">
<h4>Metabolic phenotypes</h4>
<ul>
<li><a href="t2d_2012.html">Type 2 diabetes (Morris et al. 2012)</a></li>
<li><a href="hr_2013.html">Heart rate (Den Hoed et al. 2013)</a></li>
<li><a href="urate_2013.html">Serum urate (Köttgen et al. 2013)</a></li>
<li><a href="cad_2015.html">Coronary artery disease (Nikpay et al. 2015)</a></li>
<li><a href="mi_2015.html">Myocardial infarction (Nikpay et al. 2015)</a></li>
</ul>
</div>
<div id="neurological-phenotypes" class="section level4">
<h4>Neurological phenotypes</h4>
<ul>
<li><a href="load_2013.html">Alzheimer’s disease (Lambert et al. 2013)</a></li>
<li><a href="scz_2014.html">Schizophrenia (Ripke et al. 2014)</a></li>
<li><a href="neu_2016.html">Neuroticism (Okbay et al. 2016)</a></li>
<li><a href="ds_2016.html">Depressive symptoms (Okbay et al. 2016)</a></li>
</ul>
</div>
</div>
<div id="additional-resources" class="section level2">
<h2>Additional resources</h2>
<div id="where-can-i-find-round-1-results-of-all-3913-pathways" class="section level4">
<h4>Where can I find “Round 1” results of all 3913 pathways?</h4>
</div>
<div id="where-can-i-find-the-gene-prioritization-results" class="section level4">
<h4>Where can I find the gene prioritization results?</h4>
</div>
</div>
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