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<h1 class="title toc-ignore">CSNA_workflow</h1>
<h4 class="author">Hao He</h4>
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<div id="TOC">
<ul>
<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-convert-them-to-a-single-big-data-frame">2 Grab intensities from GeneSeek FinalReport.txt files convert them to a single big data frame</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="#plot-the-recombination-block-size-and-founder-props-across-all-generations">7 Plot the recombination block size and founder props across all generations</a></li>
<li><a href="#gcta-heritability">8 GCTA heritability</a></li>
<li><a href="#qtl-mapping">9 qtl mapping</a></li>
<li><a href="#qtl-permutation">10 qtl permutation</a></li>
<li><a href="#qtl-blup">11 qtl blup</a></li>
<li><a href="#plot-qtl-mapping">12 plot qtl mapping</a></li>
<li><a href="#conditional_m2_qtlmapping">13 conditional_m2_qtlmapping</a></li>
<li><a href="#geneseek2qtl2fst_gagnon">14 geneseek2qtl2fst_Gagnon</a></li>
<li><a href="#firstgm2genoprobs_gagnon">15 firstgm2genoprobs_Gagnon</a></li>
<li><a href="#diagnosis_qc_gigamuga_gagnon">16 diagnosis_qc_gigamuga_gagnon</a></li>
</ul>
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<strong>Last updated:</strong> 2020-11-04
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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
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<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>
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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.
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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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<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongRepositoryversionstrongahrefhttpsgithubcomTheJacksonLaboratoryCSNAtree9a8cab2ee1602508942cf92c453d34aad7873687targetblank9a8cab2a"> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> <strong>Repository version:</strong> <a href="https://github.com/TheJacksonLaboratory/CSNA/tree/9a8cab2ee1602508942cf92c453d34aad7873687" target="_blank">9a8cab2</a> </a>
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Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.
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<p>
The results in this page were generated with repository version <a href="https://github.com/TheJacksonLaboratory/CSNA/tree/9a8cab2ee1602508942cf92c453d34aad7873687" target="_blank">9a8cab2</a>. See the <em>Past versions</em> tab to see a history of the changes made to the R Markdown and HTML files.
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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:
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html
</td>
<td>
<a href="https://rawcdn.githack.com/TheJacksonLaboratory/CSNA/d977cdc19eab6afa2b4d05fc9e88456424436b82/docs/index.html" target="_blank">d977cdc</a>
</td>
<td>
xhyuo
</td>
<td>
2020-02-16
</td>
<td>
Build site.
</td>
</tr>
<tr>
<td>
html
</td>
<td>
<a href="https://rawcdn.githack.com/TheJacksonLaboratory/CSNA/6861ae73fa9c54567eec7190f86b62f9827f303f/docs/index.html" target="_blank">6861ae7</a>
</td>
<td>
xhyuo
</td>
<td>
2020-02-16
</td>
<td>
Build site.
</td>
</tr>
<tr>
<td>
html
</td>
<td>
<a href="https://rawcdn.githack.com/TheJacksonLaboratory/CSNA/a2f202a3bf3f23ec2323e324d0b64fbbaccecae0/docs/index.html" target="_blank">a2f202a</a>
</td>
<td>
xhyuo
</td>
<td>
2020-01-09
</td>