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<h1 class="title toc-ignore">CSNA_workflow</h1>
<h4 class="author"><em>Hao He</em></h4>

</div>

<div id="TOC">
<ul>
<li><a href="#data-transformation-from-finalreport.txt-to-qtl2-for-11-batches-of-jackson_lab_bubier">1 Data transformation from Finalreport.txt to qtl2 for 11 batches of Jackson_Lab_Bubier</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-batches">4 Genotype diagnostics for diversity outbred mice of 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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<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="#checks"> Checks <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> </a>
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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
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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>
</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.
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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>
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<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongRepositoryversionstrongahrefhttpsgithubcomTheJacksonLaboratoryCSNAtree2fa487b82bfe428508a7f03b96b41eb8e27fcaf3targetblank2fa487ba"> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> <strong>Repository version:</strong> <a href="https://github.com/TheJacksonLaboratory/CSNA/tree/2fa487b82bfe428508a7f03b96b41eb8e27fcaf3" target="_blank">2fa487b</a> </a>
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<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>
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2019-09-22
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<a href="https://github.com/TheJacksonLaboratory/CSNA/blob/898ff80e7a88c046ed3b5a1fabac19eaf3a71ef3/analysis/index.Rmd" target="_blank">898ff80</a>
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2019-09-22
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Start workflowr project.
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</div>
<hr>
</div>
</div>
</div>
<div id="data-transformation-from-finalreport.txt-to-qtl2-for-11-batches-of-jackson_lab_bubier" class="section level3">
<h3>1 Data transformation from Finalreport.txt to qtl2 for 11 batches of Jackson_Lab_Bubier</h3>
<ul>
<li>[01_geneseek2qtl2.R]</li>
</ul>
</div>
<div id="grab-intensities-from-geneseek-finalreport.txt-files-convert-them-to-a-single-big-data-frame" class="section level3">
<h3>2 Grab intensities from GeneSeek FinalReport.txt files convert them to a single big data frame</h3>
<ul>
<li>[02_geneseek2intensity.R]</li>
</ul>
</div>
<div id="first-time-to-calculate-genoprobs-maxmarg-crossover-errorlod-snpg-for-the-qc-diagnositics" class="section level3">
<h3>3 First time to calculate genoprobs, maxmarg, crossover, errorlod, snpg for the qc diagnositics</h3>
<ul>
<li>[03_firstgm2genoprobs.R]</li>
</ul>
</div>
<div id="genotype-diagnostics-for-diversity-outbred-mice-of-batches" class="section level3">
<h3>4 Genotype diagnostics for diversity outbred mice of batches</h3>
<ul>
<li><a href="04_diagnosis_qc_gigamuga_nine_batches.html">04_diagnosis_qc_gigamuga_nine_batches.Rmd</a></li>
<li><a href="04_diagnosis_qc_gigamuga_11_batches.html">04_diagnosis_qc_gigamuga_11_batches.Rmd</a></li>
</ul>
</div>
<div id="after-qc-genotype-diagnostics" class="section level3">
<h3>5 After QC, genotype diagnostics</h3>
<ul>
<li><a href="05_after_diagnosis_qc_gigamuga_nine_batches.html">05_after_diagnosis_qc_gigamuga_nine_batches.Rmd</a></li>
<li><a href="05_after_diagnosis_qc_gigamuga_11_batches.html">05_after_diagnosis_qc_gigamuga_11_batches.Rmd</a></li>
</ul>
</div>
<div id="calculation-of-the-genoprobs-after-qc-and-do-interpolatino-to-69k-grid" class="section level3">
<h3>6 Calculation of the genoprobs after qc and do interpolatino to 69K grid</h3>
<ul>
<li>[06_final_pr_apr_69K.R]</li>
</ul>
</div>
<div id="plot-the-recombination-block-size-and-founder-props-across-all-generations" class="section level3">
<h3>7 Plot the recombination block size and founder props across all generations</h3>
<ul>
<li><a href="07_recomb_size_founder_prop.html">07_recomb_size_founder_prop.Rmd</a></li>
</ul>
</div>
<div id="gcta-heritability" class="section level3">
<h3>8 GCTA heritability</h3>
<ul>
<li>[08_gcta_herit.R]</li>
</ul>
</div>
<div id="qtl-mapping" class="section level3">
<h3>9 qtl mapping</h3>
<ul>
<li>[09_qtlmapping.R]</li>
</ul>
</div>
<div id="qtl-permutation" class="section level3">
<h3>10 qtl permutation</h3>
<ul>
<li>[10_qtl_permu.R]</li>
</ul>
</div>
<div id="qtl-blup" class="section level3">
<h3>11 qtl blup</h3>
<ul>
<li>[11_qtl_blup.R]</li>
</ul>
</div>
<div id="plot-qtl-mapping" class="section level3">
<h3>12 plot qtl mapping</h3>
<ul>
<li><a href="12_plot_qtl_mapping_1.html">12_plot_qtl_mapping_1.Rmd</a></li>
<li><a href="12_plot_qtl_mapping_2.html">12_plot_qtl_mapping_2.Rmd</a></li>
<li><a href="12_plot_69k_qtl_mapping_2.html">12_plot_69k_qtl_mapping_2.Rmd</a></li>
</ul>
</div>
<div id="conditional_m2_qtlmapping" class="section level3">
<h3>13 conditional_m2_qtlmapping</h3>
<ul>
<li>[13_conditional_m2_qtlmapping.R]</li>
<li><a href="13_plot_conditional_m2_qtlmapping.html">13_plot_conditional_m2_qtlmapping.Rmd</a></li>
</ul>
</div>
<div id="geneseek2qtl2fst_gagnon" class="section level3">
<h3>14 geneseek2qtl2fst_Gagnon</h3>
<ul>
<li>[14_geneseek2qtl2fst_Gagnon.R]</li>
</ul>
</div>
<div id="firstgm2genoprobs_gagnon" class="section level3">
<h3>15 firstgm2genoprobs_Gagnon</h3>
<ul>
<li>[15_firstgm2genoprobs_Gagnon.R]</li>
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<div id="diagnosis_qc_gigamuga_gagnon" class="section level3">
<h3>16 diagnosis_qc_gigamuga_gagnon</h3>
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<li><a href="16_diagnosis_qc_gigamuga_gagnon.html">16_diagnosis_qc_gigamuga_gagnon.Rmd</a></li>
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