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<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8" />
<meta name="generator" content="pandoc" />
<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
<meta name="author" content="Developed and maintained by Hao He (hao.he@jax.org)" />
<title>CSNA_workflow</title>
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<div class="container">
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<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
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<h1 class="title toc-ignore">CSNA_workflow</h1>
<h4 class="author">Developed and maintained by Hao He (<a href="mailto:hao.he@jax.org" class="email">hao.he@jax.org</a>)</h4>
</div>
<div id="TOC">
<ul>
<li><a href="#process-all-phenotypes-in-founder-cc-and-do">0 Process all phenotypes in founder CC and DO</a></li>
<li><a href="#data-transformation-from-finalreport.txt-to-qtl2-for-12-batches">1 Data transformation from Finalreport.txt to qtl2 for 12 batches</a></li>
<li><a href="#grab-intensities-from-geneseek-finalreport.txt-files">2 Grab intensities from GeneSeek FinalReport.txt files</a></li>
<li><a href="#first-time-to-calculate-genoprobs-maxmarg-crossover-errorlod-snpg-for-the-qc-diagnositics">3 First time to calculate genoprobs, maxmarg, crossover, errorlod, snpg for the qc diagnositics</a></li>
<li><a href="#genotype-diagnostics-for-diversity-outbred-mice-of-12-batches">4 Genotype diagnostics for diversity outbred mice of 12 batches</a></li>
<li><a href="#after-qc-genotype-diagnostics">5 After QC, genotype diagnostics</a></li>
<li><a href="#calculation-of-the-genoprobs-after-qc-and-do-interpolatino-to-69k-grid">6 Calculation of the genoprobs after qc and do interpolatino to 69K grid</a></li>
<li><a href="#do-diversity-report">7 DO Diversity Report</a></li>
<li><a href="#gcta-heritability">8 GCTA heritability</a></li>
<li><a href="#reverse-learning-project">Reverse learning project</a></li>
</ul>
</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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<a data-toggle="tab" href="#versions">Past versions</a>
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<div id="summary" class="tab-pane fade in active">
<p>
<strong>Last updated:</strong> 2022-09-16
</p>
<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 1.6.2). 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>
<hr>
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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>
</p>
</div>
<div id="strongRMarkdownfilestronguptodate" class="panel-collapse collapse">
<div class="panel-body">
<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>
<div class="panel panel-default">
<div class="panel-heading">
<p class="panel-title">
<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongRepositoryversionstrongahrefhttpsghpdrKylw4hMKNJU2lQgUoU1pPwJIkipy1vf4qZgithubcomTheJacksonLaboratoryCSNAtreeb8db415d13f4cde54d1e82147e49ee644bbbca86targetblankb8db415a"> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> <strong>Repository version:</strong> <a href="https://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@github.com/TheJacksonLaboratory/CSNA/tree/b8db415d13f4cde54d1e82147e49ee644bbbca86" target="_blank">b8db415</a> </a>
</p>
</div>
<div id="strongRepositoryversionstrongahrefhttpsghpdrKylw4hMKNJU2lQgUoU1pPwJIkipy1vf4qZgithubcomTheJacksonLaboratoryCSNAtreeb8db415d13f4cde54d1e82147e49ee644bbbca86targetblankb8db415a" class="panel-collapse collapse">
<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.
</p>
<p>
The results in this page were generated with repository version <a href="https://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@github.com/TheJacksonLaboratory/CSNA/tree/b8db415d13f4cde54d1e82147e49ee644bbbca86" target="_blank">b8db415</a>. See the <em>Past versions</em> tab to see a history of the changes made to the R Markdown and HTML files.
</p>
<p>
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>
Ignored files:
Ignored: .Rhistory
Ignored: .Rproj.user/
Ignored: output/qtlmapping/
Untracked files:
Untracked: analysis/.nfs0000000135a08b9b00002448
Untracked: analysis/.nfs0000000135a08ba50000244a
Untracked: analysis/Prj01_RL_pheno_qtl2_DO_11092020_69k.sh
Untracked: analysis/Prj01_RL_pheno_qtl2_DO_11092020_69k.stderr
Untracked: analysis/Prj01_RL_pheno_qtl2_DO_11092020_69k.stdout
Untracked: analysis/RL_h2.R
Untracked: analysis/csna_image.sif
Untracked: analysis/draft.R
Untracked: analysis/for_johnathan.R
Untracked: analysis/index0.Rmd
Untracked: analysis/meta_robyn.R
Untracked: analysis/meta_robyn_Jentsch2.R
Untracked: analysis/meta_robyn_Price.R
Untracked: analysis/meta_robyn_cc.R
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<a href="https://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@github.com/TheJacksonLaboratory/CSNA/blob/553d37f7570807b5fea5a23b72f7512cd0597bfe/analysis/index.Rmd" target="_blank">553d37f</a>
</td>
<td>
xhyuo
</td>
<td>
2020-11-06
</td>
<td>
12_batches_report
</td>
</tr>
<tr>
<td>
html
</td>
<td>
<a href="https://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@github.com/TheJacksonLaboratory/CSNA/blob/6610ab11997a53243da6e98b15bea0b4aaabc5e2/docs/index.html" target="_blank">6610ab1</a>