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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="#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>
</ul>
</div>

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<p>
<strong>Last updated:</strong> 2021-03-15
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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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<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.
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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="#strongRepositoryversionstrongahrefhttpsgithubcomTheJacksonLaboratoryCSNAtreefd9720d435774de6687958a9091a1f8bbac40955targetblankfd9720da"> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> <strong>Repository version:</strong> <a href="https://github.com/TheJacksonLaboratory/CSNA/tree/fd9720d435774de6687958a9091a1f8bbac40955" target="_blank">fd9720d</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.
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<p>
The results in this page were generated with repository version <a href="https://github.com/TheJacksonLaboratory/CSNA/tree/fd9720d435774de6687958a9091a1f8bbac40955" target="_blank">fd9720d</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/

Untracked files:
    Untracked:  analysis/.nfs0000000135a08b9b00002448
    Untracked:  analysis/.nfs0000000135a08ba50000244a
    Untracked:  analysis/csna_image.sif
    Untracked:  analysis/index0.Rmd
    Untracked:  analysis/rstudio.4.0.3.simg
    Untracked:  analysis/scripts/
    Untracked:  analysis/workflow_proc.R
    Untracked:  analysis/workflow_proc.sh
    Untracked:  analysis/workflow_proc.stderr
    Untracked:  analysis/workflow_proc.stdout
    Untracked:  archived/
    Untracked:  code/FinalReport2Plink.sh
    Untracked:  code/csna_qtlmapping_workflow.R
    Untracked:  code/reconst_utils.R
    Untracked:  data/69k_grid_pgmap.RData
    Untracked:  data/FinalReport/
    Untracked:  data/GCTA/
    Untracked:  data/GM/
    Untracked:  data/Jackson_Lab_11_batches/
    Untracked:  data/Jackson_Lab_12_batches/
    Untracked:  data/Jackson_Lab_Bubier_MURGIGV01/
    Untracked:  data/Jackson_Lab_Gagnon/
    Untracked:  data/RTG/
    Untracked:  data/cc_do_founders_key.rds
    Untracked:  data/cc_variants.sqlite
    Untracked:  data/marker_grid_0.02cM_plus.txt
    Untracked:  data/mouse_genes_mgi.sqlite
    Untracked:  data/pheno/
    Untracked:  output/archived_output/
    Untracked:  output/pdf/
    Untracked:  output/qtlmapping/

Unstaged changes:
    Modified:   .Rprofile
    Modified:   .gitignore
    Modified:   README.md
    Modified:   _workflowr.yml
    Deleted:    analysis/01_geneseek2qtl2.R
    Deleted:    analysis/02_geneseek2intensity.R
    Deleted:    analysis/03_firstgm2genoprobs.R
    Deleted:    analysis/04_diagnosis_qc_gigamuga_11_batches.Rmd
    Modified:   analysis/04_diagnosis_qc_gigamuga_12_batches.Rmd
    Deleted:    analysis/04_diagnosis_qc_gigamuga_nine_batches.R
    Deleted:    analysis/04_diagnosis_qc_gigamuga_nine_batches.Rmd
    Deleted:    analysis/05_after_diagnosis_qc_gigamuga_11_batches.Rmd
    Modified:   analysis/05_after_diagnosis_qc_gigamuga_12_batches.Rmd
    Deleted:    analysis/05_after_diagnosis_qc_gigamuga_nine_batches.R
    Deleted:    analysis/05_after_diagnosis_qc_gigamuga_nine_batches.Rmd
    Deleted:    analysis/06_final_pr_apr_69K.R
    Deleted:    analysis/07.1_html_founder_prop.R
    Modified:   analysis/07_do_diversity_report.Rmd
    Deleted:    analysis/07_recomb_size_founder_prop.R
    Deleted:    analysis/07_recomb_size_founder_prop.Rmd
    Deleted:    analysis/08_gcta_herit.R
    Deleted:    analysis/09_qtlmapping.R
    Deleted:    analysis/10_qtl_permu.R
    Deleted:    analysis/11_qtl_blup.R
    Deleted:    analysis/12_plot_69k_qtl_mapping_2.Rmd
    Deleted:    analysis/12_plot_qtl_mapping_1.Rmd
    Deleted:    analysis/12_plot_qtl_mapping_2.Rmd
    Deleted:    analysis/13_plot_69k_conditional_m2_qtlmapping.Rmd
    Deleted:    analysis/13_plot_conditional_m2_qtlmapping.Rmd
    Deleted:    analysis/16_diagnosis_qc_gigamuga_gagnon.Rmd
    Deleted:    analysis/16_diagnosis_qc_gigamuga_gagnon2.Rmd
    Deleted:    analysis/17_plot_qtl_mapping.Rmd
    Modified:   analysis/_site.yml
    Deleted:    analysis/run_01_geneseek2qtl2.R
    Deleted:    analysis/run_02_geneseek2intensity.R
    Deleted:    analysis/run_03_firstgm2genoprobs.R
    Deleted:    analysis/run_04_diagnosis_qc_gigamuga_nine_batches.R
    Deleted:    analysis/run_05_after_diagnosis_qc_gigamuga_nine_batches.R
    Deleted:    analysis/run_06_final_pr_apr_69K.R
    Deleted:    analysis/run_07.1_html_founder_prop.R
    Deleted:    analysis/run_07_recomb_size_founder_prop.R
    Deleted:    analysis/run_08_gcta_herit.R
    Deleted:    analysis/run_09_qtlmapping.R
    Deleted:    analysis/run_10_qtl_permu.R
    Deleted:    analysis/run_11_qtl_blup.R
    Modified:   code/README.md
    Modified:   csna_workflow.Rproj
    Modified:   data/README.md
    Modified:   output/README.md

</code></pre>
<p>
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.
</p>
</div>
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<hr>
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<div id="versions" class="tab-pane fade">

<p>
These are the previous versions of the repository in which changes were made to the R Markdown (<code>analysis/index.Rmd</code>) and HTML (<code>docs/index.html</code>) files. If you’ve configured a remote Git repository (see <code>?wflow_git_remote</code>), click on the hyperlinks in the table below to view the files as they were in that past version.
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<a href="https://github.com/TheJacksonLaboratory/CSNA/blob/fd9720d435774de6687958a9091a1f8bbac40955/analysis/index.Rmd" target="_blank">fd9720d</a>
</td>
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xhyuo
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2021-03-15
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<a href="https://github.com/TheJacksonLaboratory/CSNA/blob/553d37f7570807b5fea5a23b72f7512cd0597bfe/analysis/index.Rmd" target="_blank">553d37f</a>
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2020-11-06
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wflow_publish(files = file)
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2019-10-02
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2019-10-02
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12_plot_qtl_mapping_1.Rmd
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2019-09-22
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2019-09-22
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xhyuo
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2019-09-22
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wflow_publish(c(“analysis/index.Rmd”, “analysis/about.Rmd”,
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xhyuo
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2019-09-22
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Start workflowr project.
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</tbody>
</table>
</div>
<hr>
</div>
</div>
</div>
<div id="process-all-phenotypes-in-founder-cc-and-do" class="section level3">
<h3>0 Process all phenotypes in founder CC and DO</h3>
<ul>
<li><a href="00_Process_all_phenotypes_in_founder_CC_DO.html">00_Process_all_phenotypes_in_founder_CC_DO.Rmd</a></li>
</ul>
</div>
<div id="data-transformation-from-finalreport.txt-to-qtl2-for-12-batches" class="section level3">
<h3>1 Data transformation from Finalreport.txt to qtl2 for 12 batches</h3>
<ul>
<li>[analysis/scripts/01_FinalReport2qtl2.R]</li>
</ul>
</div>
<div id="grab-intensities-from-geneseek-finalreport.txt-files" class="section level3">
<h3>2 Grab intensities from GeneSeek FinalReport.txt files</h3>
<ul>
<li>[analysis/scripts/02_FinalReport2intensity.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>[analysis/scripts/03_firstgm2genoprobs.R]</li>
</ul>
</div>
<div id="genotype-diagnostics-for-diversity-outbred-mice-of-12-batches" class="section level3">
<h3>4 Genotype diagnostics for diversity outbred mice of 12 batches</h3>
<ul>
<li><a href="04_diagnosis_qc_gigamuga_12_batches.html">04_diagnosis_qc_gigamuga_12_batches.Rmd</a></li>
<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_12_batches.html">05_after_diagnosis_qc_gigamuga_12_batches.Rmd</a></li>
<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>[analysis/scripts/06_final_pr_apr_69K.R]</li>
</ul>
</div>
<div id="do-diversity-report" class="section level3">
<h3>7 DO Diversity Report</h3>
<ul>
<li>[analysis/scripts/07_do_diversity_report.R]</li>
<li><a href="07_do_diversity_report.html">07_do_diversity_report.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>


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