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18 changes: 8 additions & 10 deletions disseminating.html
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</ul><div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/js2264/OHCA/edit/main/disseminating.qmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/js2264/OHCA/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
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<h1 class="title">
<span class="chapter-number">8</span>&nbsp; <span class="chapter-title">Data gateways: accessing public Hi-C data portals</span>
</h1>
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<p>The Hi-C experimental approach has gained significant traction across multiple fields related to genome biology, and several consortia developed large-scale programs based on this technique. The <code>fourDNData</code> and <code>DNAZooData</code> R packages were designed to accelerate the investigation of chromatin structure using these public resources.</p>
<section id="dn-data-portal" class="level2" data-number="8.1"><h2 data-number="8.1" class="anchored" data-anchor-id="dn-data-portal">
<section id="dn-data-portal" class="level2 page-columns page-full" data-number="8.1"><h2 data-number="8.1" class="anchored" data-anchor-id="dn-data-portal">
<span class="header-section-number">8.1</span> 4DN data portal</h2>
<p>The 4D Nucleome Data Coordination and Integration Center (<a href="http://dcic.4dnucleome.org/">DCIC</a>) has developed and actively maintains a <a href="https://data.4dnucleome.org/browse">data portal</a> providing public access to a wealth of resources to investigate 3D chromatin architecture. Notably, 3D chromatin conformation libraries relying on different technologies (“in situ” or “dilution” Hi-C, Capture Hi-C, Micro-C, DNase Hi-C, …), generated by 50+ collaborating labs, were homogenously processed, yielding more than 350 sets of processed files.</p>
<p><code>fourDNData</code> (read <em>4DN-Data</em>) is a package giving programmatic access to these uniformly processed Hi-C contact files.</p>
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<span><span class="co">## 4DNES18BMU79 insulation 7.18 mouse in situ Hi-C DpnII Hi-C on Mouse Olfactory System cells Mature olfactory sensory neurons with conditional Ldb1 knockout olfactory receptor cell primary cell Monahan K et al. (2019) https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/d1f4beb9-701f-4188-abe2-6271fe658770/4DNFIXKKNMS7.bw</span></span>
<span><span class="co">## 4DNES18BMU79 compartments 0.18 mouse in situ Hi-C DpnII Hi-C on Mouse Olfactory System cells Mature olfactory sensory neurons with conditional Ldb1 knockout olfactory receptor cell primary cell Monahan K et al. (2019) https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/3d429647-51c8-4e3a-a18b-eec0b1480905/4DNFIN13N8C1.bw</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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<section id="querying-individual-files" class="level3" data-number="8.1.1"><h3 data-number="8.1.1" class="anchored" data-anchor-id="querying-individual-files">
<section id="querying-individual-files" class="level3 page-columns page-full" data-number="8.1.1"><h3 data-number="8.1.1" class="anchored" data-anchor-id="querying-individual-files">
<span class="header-section-number">8.1.1</span> Querying individual files</h3>
<p>The <code><a href="https://rdrr.io/pkg/fourDNData/man/fourDNData.html">fourDNData()</a></code> function can be used to directly fetch specific files from the 4DN data portal:</p>
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<li>
<code>type = 'insulation'</code> will fetch a <code>.bigwig</code> track file precomputed by the 4DN consortium. This track corresponds to the genome-wide insulation score computed by <code>cooltools</code> as described in <span class="citation" data-cites="Crane_2015">Crane et al. (<a href="interoperability.html#ref-Crane_2015" role="doc-biblioref">2015</a>)</span>. To know more about this, read <a href="https://data.4dnucleome.org/resources/data-analysis/insulation_compartment_scores#insulation_scores_and_boundaries_page_all">the excerpt from 4DN data portal</a>. Once fetched from the 4DN data portal, the local file can be imported in <code>R</code> using the <code>import</code> function, which will generate a <code>RleList</code> object.</li>
</ul>
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<div class="no-row-height column-margin column-container"><div id="ref-Crane_2015" class="csl-entry" role="listitem">
Crane, E., Bian, Q., McCord, R. P., Lajoie, B. R., Wheeler, B. S., Ralston, E. J., Uzawa, S., Dekker, J., &amp; Meyer, B. J. (2015). Condensin-driven remodelling of x chromosome topology during dosage compensation. <em>Nature</em>, <em>523</em>(7559), 240–244. <a href="https://doi.org/10.1038/nature14450">https://doi.org/10.1038/nature14450</a>
</div></div><div class="cell" data-layout-align="center" data-hash="disseminating_cache/html/unnamed-chunk-6_d5634a6345d6486d15a775e7526591b6">
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/fourDNData/man/fourDNData.html">fourDNData</a></span><span class="op">(</span>experimentSetAccession <span class="op">=</span> <span class="st">'4DNES25ABNZ1'</span>, type <span class="op">=</span> <span class="st">'insulation'</span><span class="op">)</span> <span class="op">|&gt;</span> </span>
<span> <span class="fu">import</span><span class="op">(</span>as <span class="op">=</span> <span class="st">'Rle'</span><span class="op">)</span></span>
<span><span class="co">## |===================================| 100%</span></span>
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</section><section id="bibliography" class="level1 unnumbered"><h1 class="unnumbered">References</h1>
<div id="refs" class="references csl-bib-body hanging-indent" data-line-spacing="2" role="list" style="display: none">
<div id="ref-Crane_2015" class="csl-entry" role="listitem">
Crane, E., Bian, Q., McCord, R. P., Lajoie, B. R., Wheeler, B. S., Ralston, E. J., Uzawa, S., Dekker, J., &amp; Meyer, B. J. (2015). Condensin-driven remodelling of x chromosome topology during dosage compensation. <em>Nature</em>, <em>523</em>(7559), 240–244. <a href="https://doi.org/10.1038/nature14450">https://doi.org/10.1038/nature14450</a>
</div>
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Expand Up @@ -523,7 +523,7 @@ <h1 class="title">Orchestrating Hi-C analysis with Bioconductor</h1>
<span><span class="co">## IRanges 2.36.0 2023-10-24 [1] Bioconductor</span></span>
<span><span class="co">## jsonlite 1.8.7 2023-06-29 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## KEGGREST 1.42.0 2023-10-24 [1] Bioconductor</span></span>
<span><span class="co">## knitr 1.44 2023-09-11 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## knitr 1.45 2023-10-30 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## later 1.3.1 2023-05-02 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## lattice 0.22-5 2023-10-24 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.3.1)</span></span>
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<span><span class="co">## rmdformats 1.0.4 2022-05-17 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## RSpectra 0.16-1 2022-04-24 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## RSQLite 2.3.2 2023-10-28 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## rstudioapi 0.15.0 2023-07-07 [1] CRAN (R 4.3.1)</span></span>
<span><span class="co">## S4Arrays 1.2.0 2023-10-24 [1] Bioconductor</span></span>
<span><span class="co">## S4Vectors 0.40.1 2023-10-26 [1] Bioconductor</span></span>
<span><span class="co">## scales 1.2.1 2022-08-20 [1] CRAN (R 4.3.1)</span></span>
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}
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<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="va">hic</span></span>
<span><span class="co">## `HiCExperiment` object with 471,364 contacts over 407 regions </span></span>
<span><span class="co">## -------</span></span>
<span><span class="co">## fileName: "/github/home/.cache/R/ExperimentHub/1a92248c093f_7752" </span></span>
<span><span class="co">## fileName: "/github/home/.cache/R/ExperimentHub/1a9466054db5_7752" </span></span>
<span><span class="co">## focus: "II" </span></span>
<span><span class="co">## resolutions(5): 1000 2000 4000 8000 16000</span></span>
<span><span class="co">## active resolution: 2000 </span></span>
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<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="va">pf</span></span>
<span><span class="co">## PairsFile object</span></span>
<span><span class="co">## resource: /github/home/.cache/R/ExperimentHub/1a92835ced9_7753</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<span><span class="co">## resource: /github/home/.cache/R/ExperimentHub/1a9456d59216_7753</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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<p>If needed, <code>PairsFile</code> connections can be imported directly into a <code>GInteractions</code> object with <code><a href="https://rdrr.io/pkg/BiocIO/man/IO.html">import()</a></code>.</p>
<div class="cell" data-layout-align="center" data-hash="interactions-centric_cache/html/unnamed-chunk-6_309f0849a61dbd929c60ddb949b1faf2">
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<div class="cell" data-layout-align="center" data-hash="interactions-centric_cache/html/unnamed-chunk-7_61a6b73bdd59d810076d1d2bca92deb1">
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/js2264/HiContacts">HiContacts</a></span><span class="op">)</span></span>
<span><span class="va">ps</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/HiContacts/man/Ps.html">distanceLaw</a></span><span class="op">(</span><span class="va">pf</span>, by_chr <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> </span>
<span><span class="co">## Importing pairs file /github/home/.cache/R/ExperimentHub/1a92835ced9_7753 in memory. This may take a while...</span></span>
<span><span class="co">## Importing pairs file /github/home/.cache/R/ExperimentHub/1a9456d59216_7753 in memory. This may take a while...</span></span>
<span><span class="va">ps</span></span>
<span><span class="co">## # A tibble: 115 × 6</span></span>
<span><span class="co">## chr binned_distance p norm_p norm_p_unity slope</span></span>
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</div>
<div class="cell" data-layout-align="center" data-hash="interactions-centric_cache/html/unnamed-chunk-9_4f0f21a4e13a6c5054d3a8c7a6ad12bc">
<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="va">eco1_ps</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/HiContacts/man/Ps.html">distanceLaw</a></span><span class="op">(</span><span class="va">eco1_pf</span>, by_chr <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> </span>
<span><span class="co">## Importing pairs file /github/home/.cache/R/ExperimentHub/21f275852cbd_7755 in memory. This may take a while...</span></span>
<span><span class="co">## Importing pairs file /github/home/.cache/R/ExperimentHub/21f428f3345_7755 in memory. This may take a while...</span></span>
<span><span class="va">eco1_ps</span></span>
<span><span class="co">## # A tibble: 115 × 6</span></span>
<span><span class="co">## chr binned_distance p norm_p norm_p_unity slope</span></span>
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<span class="header-section-number">6.4</span> Scalograms</h2>
<p>Scalograms were introduced in <span class="citation" data-cites="Lioy_2018">Lioy et al. (<a href="interoperability.html#ref-Lioy_2018" role="doc-biblioref">2018</a>)</span> to investigate distance-dependent contact frequencies for individual genomic bins along chromosomes.<br>
To generate a scalogram, one needs to provide a <code>HiCExperiment</code> object with a valid associated <code>pairsFile</code>.</p>
<div class="cell" data-layout-align="center" data-hash="interactions-centric_cache/html/unnamed-chunk-16_320af3e0978383b398fae450d37c1a1d">
<div class="no-row-height column-margin column-container"><div id="ref-Lioy_2018" class="csl-entry" role="listitem">
Lioy, V. S., Cournac, A., Marbouty, M., Duigou, S., Mozziconacci, J., Espéli, O., Boccard, F., &amp; Koszul, R. (2018). Multiscale structuring of the e.&nbsp;Coli chromosome by nucleoid-associated and condensin proteins. <em>Cell</em>, <em>172</em>(4), 771–783.e18. <a href="https://doi.org/10.1016/j.cell.2017.12.027">https://doi.org/10.1016/j.cell.2017.12.027</a>
</div></div><div class="cell" data-layout-align="center" data-hash="interactions-centric_cache/html/unnamed-chunk-16_320af3e0978383b398fae450d37c1a1d">
<div class="sourceCode" id="cb19"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/HiCExperiment/man/AllGenerics.html">pairsFile</a></span><span class="op">(</span><span class="va">hic</span><span class="op">)</span> <span class="op">&lt;-</span> <span class="va">pairsf</span></span>
<span><span class="va">scalo</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/HiContacts/man/scalogram.html">scalogram</a></span><span class="op">(</span><span class="va">hic</span><span class="op">)</span> </span>
<span><span class="co">## Importing pairs file /github/home/.cache/R/ExperimentHub/1a92835ced9_7753 in memory. This may take a while...</span></span>
<span><span class="co">## Importing pairs file /github/home/.cache/R/ExperimentHub/1a9456d59216_7753 in memory. This may take a while...</span></span>
<span><span class="fu"><a href="https://rdrr.io/pkg/HiContacts/man/plotScalogram.html">plotScalogram</a></span><span class="op">(</span><span class="va">scalo</span> <span class="op">|&gt;</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span><span class="op">(</span><span class="va">chr</span> <span class="op">==</span> <span class="st">'II'</span><span class="op">)</span>, ylim <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="fl">1e3</span>, <span class="fl">1e5</span><span class="op">)</span><span class="op">)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output-display">
<div class="quarto-figure quarto-figure-center">
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<span><span class="co">## loading from cache</span></span>
<span><span class="fu"><a href="https://rdrr.io/pkg/HiCExperiment/man/AllGenerics.html">pairsFile</a></span><span class="op">(</span><span class="va">eco1_hic</span><span class="op">)</span> <span class="op">&lt;-</span> <span class="va">eco1_pairsf</span></span>
<span><span class="va">eco1_scalo</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/HiContacts/man/scalogram.html">scalogram</a></span><span class="op">(</span><span class="va">eco1_hic</span><span class="op">)</span> </span>
<span><span class="co">## Importing pairs file /github/home/.cache/R/ExperimentHub/21f275852cbd_7755 in memory. This may take a while...</span></span>
<span><span class="co">## Importing pairs file /github/home/.cache/R/ExperimentHub/21f428f3345_7755 in memory. This may take a while...</span></span>
<span><span class="va">merged_scalo</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/BiocGenerics/man/cbind.html">rbind</a></span><span class="op">(</span></span>
<span> <span class="va">scalo</span> <span class="op">|&gt;</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span><span class="op">(</span>sample <span class="op">=</span> <span class="st">'WT'</span><span class="op">)</span>, </span>
<span> <span class="va">eco1_scalo</span> <span class="op">|&gt;</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span><span class="op">(</span>sample <span class="op">=</span> <span class="st">'eco1'</span><span class="op">)</span></span>
Expand All @@ -660,11 +662,7 @@ <h1 class="title">


</section><section id="bibliography" class="level1 unnumbered"><h1 class="unnumbered">References</h1>
<div id="refs" class="references csl-bib-body hanging-indent" data-line-spacing="2" role="list" style="display: none">
<div id="ref-Lioy_2018" class="csl-entry" role="listitem">
Lioy, V. S., Cournac, A., Marbouty, M., Duigou, S., Mozziconacci, J., Espéli, O., Boccard, F., &amp; Koszul, R. (2018). Multiscale structuring of the e.&nbsp;Coli chromosome by nucleoid-associated and condensin proteins. <em>Cell</em>, <em>172</em>(4), 771–783.e18. <a href="https://doi.org/10.1016/j.cell.2017.12.027">https://doi.org/10.1016/j.cell.2017.12.027</a>
</div>
</div>

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