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docs/devel/index.html

@@ -668,7 +668,7 @@ <h1 class="title">Orchestrating Hi-C analysis with Bioconductor</h1>
 <span><span class="co">##   munsell                       0.5.0      2018-06-12 [2] CRAN (R 4.4.0)</span></span>
 <span><span class="co">##   nlme                          3.1-163    2023-08-09 [3] CRAN (R 4.4.0)</span></span>
 <span><span class="co">##   nnet                          7.3-19     2023-05-03 [3] CRAN (R 4.4.0)</span></span>
-<span><span class="co">##   OHCA                          0.99.0     2023-11-07 [1] local</span></span>
+<span><span class="co">##   OHCA                          0.99.0     2023-11-07 [1] Bioconductor</span></span>
 <span><span class="co">##   openssl                       2.1.1      2023-09-25 [2] CRAN (R 4.4.0)</span></span>
 <span><span class="co">##   OrganismDbi                   1.45.0     2023-10-25 [2] Bioconductor</span></span>
 <span><span class="co">##   packrat                       0.9.2      2023-09-05 [2] CRAN (R 4.4.0)</span></span>
@@ -798,7 +798,7 @@ <h1 class="title">Orchestrating Hi-C analysis with Bioconductor</h1>
 <span><span class="co">##   zip                           2.3.0      2023-04-17 [2] CRAN (R 4.4.0)</span></span>
 <span><span class="co">##   zlibbioc                      1.49.0     2023-10-24 [2] Bioconductor</span></span>
 <span><span class="co">##  </span></span>
-<span><span class="co">##   [1] /tmp/RtmpEEUcH8/Rinst555f2f89bc</span></span>
+<span><span class="co">##   [1] /tmp/RtmpVQDQnT/Rinst55b2b1d77</span></span>
 <span><span class="co">##   [2] /usr/local/lib/R/site-library</span></span>
 <span><span class="co">##   [3] /usr/local/lib/R/library</span></span>
 <span><span class="co">##  </span></span>

docs/devel/pages/data-representation.html

@@ -1572,7 +1572,7 @@ <h1 class="title">
 <div class="cell" data-layout-align="center">
 <div class="sourceCode" id="cb47"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="va">coolf</span></span>
 <span><span class="co">##                                           EH7702 </span></span>
-<span><span class="co">##  "/root/.cache/R/ExperimentHub/174688ce76a_7752"</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<span><span class="co">##  "/root/.cache/R/ExperimentHub/1747aa0ffd6_7752"</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </div>
 <p>Similarly, example files are available for other file formats:</p>
 <div class="cell" data-layout-align="center">
@@ -1642,15 +1642,15 @@ <h1 class="title">
 <span><span class="co"># ----- This creates a connection to a `.(m)cool` file (path stored in `coolf`)</span></span>
 <span><span class="fu"><a href="https://rdrr.io/pkg/HiCExperiment/man/CoolFile-class.html">CoolFile</a></span><span class="op">(</span><span class="va">coolf</span><span class="op">)</span></span>
 <span><span class="co">##  CoolFile object</span></span>
-<span><span class="co">##  .mcool file: /root/.cache/R/ExperimentHub/174688ce76a_7752 </span></span>
+<span><span class="co">##  .mcool file: /root/.cache/R/ExperimentHub/1747aa0ffd6_7752 </span></span>
 <span><span class="co">##  resolution: 1000 </span></span>
 <span><span class="co">##  pairs file: </span></span>
 <span><span class="co">##  metadata(0):</span></span>
 <span></span>
 <span><span class="co"># ----- This creates a connection to a `.hic` file (path stored in `hicf`)</span></span>
 <span><span class="fu"><a href="https://rdrr.io/pkg/HiCExperiment/man/HicFile-class.html">HicFile</a></span><span class="op">(</span><span class="va">hicf</span><span class="op">)</span></span>
 <span><span class="co">##  HicFile object</span></span>
-<span><span class="co">##  .hic file: /root/.cache/R/ExperimentHub/17460f12195_7836 </span></span>
+<span><span class="co">##  .hic file: /root/.cache/R/ExperimentHub/1747a133ab3_7836 </span></span>
 <span><span class="co">##  resolution: 1000 </span></span>
 <span><span class="co">##  pairs file: </span></span>
 <span><span class="co">##  metadata(0):</span></span>
@@ -1659,16 +1659,16 @@ <h1 class="title">
 <span><span class="fu"><a href="https://rdrr.io/pkg/HiCExperiment/man/HicproFile-class.html">HicproFile</a></span><span class="op">(</span><span class="va">hicpromatrixf</span>, <span class="va">hicproregionsf</span><span class="op">)</span></span>
 <span><span class="co">##  HicproFile object</span></span>
 <span><span class="co">##  HiC-Pro files:</span></span>
-<span><span class="co">##    $ matrix:   /root/.cache/R/ExperimentHub/1745c1383e1_7837 </span></span>
-<span><span class="co">##    $ regions:  /root/.cache/R/ExperimentHub/17439b9b892_7838 </span></span>
+<span><span class="co">##    $ matrix:   /root/.cache/R/ExperimentHub/1746681cf08_7837 </span></span>
+<span><span class="co">##    $ regions:  /root/.cache/R/ExperimentHub/174132e5e85_7838 </span></span>
 <span><span class="co">##  resolution: 1000 </span></span>
 <span><span class="co">##  pairs file: </span></span>
 <span><span class="co">##  metadata(0):</span></span>
 <span></span>
 <span><span class="co"># ----- This creates a connection to a pairs file</span></span>
 <span><span class="fu"><a href="https://rdrr.io/pkg/HiCExperiment/man/PairsFile-class.html">PairsFile</a></span><span class="op">(</span><span class="va">pairsf</span><span class="op">)</span></span>
 <span><span class="co">##  PairsFile object</span></span>
-<span><span class="co">##  resource: /root/.cache/R/ExperimentHub/174ff8a7b2_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: /root/.cache/R/ExperimentHub/174733eb553_7753</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </div>
 </section><section id="contactfile-slots" class="level3" data-number="2.3.3"><h3 data-number="2.3.3" class="anchored" data-anchor-id="contactfile-slots">
 <span class="header-section-number">2.3.3</span> <code>ContactFile</code> slots</h3>
@@ -1684,7 +1684,7 @@ <h1 class="title">
 <div class="sourceCode" id="cb51"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="va">cf</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/HiCExperiment/man/CoolFile-class.html">CoolFile</a></span><span class="op">(</span><span class="va">coolf</span><span class="op">)</span></span>
 <span><span class="va">cf</span></span>
 <span><span class="co">##  CoolFile object</span></span>
-<span><span class="co">##  .mcool file: /root/.cache/R/ExperimentHub/174688ce76a_7752 </span></span>
+<span><span class="co">##  .mcool file: /root/.cache/R/ExperimentHub/1747aa0ffd6_7752 </span></span>
 <span><span class="co">##  resolution: 1000 </span></span>
 <span><span class="co">##  pairs file: </span></span>
 <span><span class="co">##  metadata(0):</span></span>
@@ -1782,7 +1782,7 @@ <h1 class="title">
 <span><span class="va">hic</span></span>
 <span><span class="co">##  `HiCExperiment` object with 8,757,906 contacts over 12,079 regions </span></span>
 <span><span class="co">##  -------</span></span>
-<span><span class="co">##  fileName: "/root/.cache/R/ExperimentHub/174688ce76a_7752" </span></span>
+<span><span class="co">##  fileName: "/root/.cache/R/ExperimentHub/1747aa0ffd6_7752" </span></span>
 <span><span class="co">##  focus: "whole genome" </span></span>
 <span><span class="co">##  resolutions(5): 1000 2000 4000 8000 16000</span></span>
 <span><span class="co">##  active resolution: 1000 </span></span>
@@ -1814,7 +1814,7 @@ <h1 class="title">
 <p>These pieces of information are called <code>slots</code>. They can be directly accessed using <code>getter</code> functions, bearing the same name than the slot.</p>
 <div class="cell" data-layout-align="center">
 <div class="sourceCode" id="cb55"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/BiocGenerics/man/fileName.html">fileName</a></span><span class="op">(</span><span class="va">hic</span><span class="op">)</span></span>
-<span><span class="co">##  [1] "/root/.cache/R/ExperimentHub/174688ce76a_7752"</span></span>
+<span><span class="co">##  [1] "/root/.cache/R/ExperimentHub/1747aa0ffd6_7752"</span></span>
 <span></span>
 <span><span class="fu"><a href="https://rdrr.io/pkg/HiCExperiment/man/AllGenerics.html">focus</a></span><span class="op">(</span><span class="va">hic</span><span class="op">)</span></span>
 <span><span class="co">##  NULL</span></span>
@@ -1881,7 +1881,7 @@ <h1 class="title">
 <span><span class="va">hic</span></span>
 <span><span class="co">##  `HiCExperiment` object with 13,681,280 contacts over 12,165 regions </span></span>
 <span><span class="co">##  -------</span></span>
-<span><span class="co">##  fileName: "/root/.cache/R/ExperimentHub/17460f12195_7836" </span></span>
+<span><span class="co">##  fileName: "/root/.cache/R/ExperimentHub/1747a133ab3_7836" </span></span>
 <span><span class="co">##  focus: "whole genome" </span></span>
 <span><span class="co">##  resolutions(5): 1000 2000 4000 8000 16000</span></span>
 <span><span class="co">##  active resolution: 1000 </span></span>
@@ -2321,14 +2321,14 @@ <h1 class="title">
 <div class="sourceCode" id="cb63"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="va">yeast_hic</span></span>
 <span><span class="co">##  `HiCExperiment` object with 8,757,906 contacts over 763 regions </span></span>
 <span><span class="co">##  -------</span></span>
-<span><span class="co">##  fileName: "/root/.cache/R/ExperimentHub/174688ce76a_7752" </span></span>
+<span><span class="co">##  fileName: "/root/.cache/R/ExperimentHub/1747aa0ffd6_7752" </span></span>
 <span><span class="co">##  focus: "whole genome" </span></span>
 <span><span class="co">##  resolutions(5): 1000 2000 4000 8000 16000</span></span>
 <span><span class="co">##  active resolution: 16000 </span></span>
 <span><span class="co">##  interactions: 267709 </span></span>
 <span><span class="co">##  scores(2): count balanced </span></span>
 <span><span class="co">##  topologicalFeatures: compartments(0) borders(0) loops(0) viewpoints(0) centromeres(16) </span></span>
-<span><span class="co">##  pairsFile: /root/.cache/R/ExperimentHub/174ff8a7b2_7753 </span></span>
+<span><span class="co">##  pairsFile: /root/.cache/R/ExperimentHub/174733eb553_7753 </span></span>
 <span><span class="co">##  metadata(3): ID org date</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </div>
 <section id="interactions" class="level4" data-number="2.4.2.1"><h4 data-number="2.4.2.1" class="anchored" data-anchor-id="interactions">
@@ -2620,8 +2620,8 @@ <h1 class="title">
 <div class="sourceCode" id="cb71"><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">yeast_hic</span><span class="op">)</span> <span class="op">&lt;-</span> <span class="va">pairsf</span></span>
 <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">yeast_hic</span><span class="op">)</span></span>
-<span><span class="co">##                                          EH7703 </span></span>
-<span><span class="co">##  "/root/.cache/R/ExperimentHub/174ff8a7b2_7753"</span></span>
+<span><span class="co">##                                           EH7703 </span></span>
+<span><span class="co">##  "/root/.cache/R/ExperimentHub/174733eb553_7753"</span></span>
 <span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/base/readLines.html">readLines</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/pkg/HiCExperiment/man/AllGenerics.html">pairsFile</a></span><span class="op">(</span><span class="va">yeast_hic</span><span class="op">)</span>, <span class="fl">25</span><span class="op">)</span></span>
 <span><span class="co">##   [1] "## pairs format v1.0"                                                             </span></span>

docs/devel/pages/interactions-centric.html

@@ -386,7 +386,7 @@ <h1 class="title">
 <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: "/root/.cache/R/ExperimentHub/174688ce76a_7752" </span></span>
+<span><span class="co">##  fileName: "/root/.cache/R/ExperimentHub/1747aa0ffd6_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>
@@ -414,7 +414,7 @@ <h1 class="title">
 <div class="cell" data-layout-align="center">
 <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: /root/.cache/R/ExperimentHub/174ff8a7b2_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: /root/.cache/R/ExperimentHub/174733eb553_7753</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </div>
 <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">
@@ -454,7 +454,7 @@ <h1 class="title">
 <div class="cell" data-layout-align="center">
 <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 /root/.cache/R/ExperimentHub/174ff8a7b2_7753 in memory. This may take a while...</span></span>
+<span><span class="co">##  Importing pairs file /root/.cache/R/ExperimentHub/174733eb553_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>
@@ -496,7 +496,7 @@ <h1 class="title">
 </div>
 <div class="cell" data-layout-align="center">
 <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 /root/.cache/R/ExperimentHub/fae489c8d53_7755 in memory. This may take a while...</span></span>
+<span><span class="co">##  Importing pairs file /root/.cache/R/ExperimentHub/fae309a2f91_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>
@@ -657,7 +657,7 @@ <h1 class="title">
 <div class="cell" data-layout-align="center">
 <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 /root/.cache/R/ExperimentHub/174ff8a7b2_7753 in memory. This may take a while...</span></span>
+<span><span class="co">##  Importing pairs file /root/.cache/R/ExperimentHub/174733eb553_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">
@@ -681,7 +681,7 @@ <h1 class="title">
 <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 /root/.cache/R/ExperimentHub/fae489c8d53_7755 in memory. This may take a while...</span></span>
+<span><span class="co">##  Importing pairs file /root/.cache/R/ExperimentHub/fae309a2f91_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>