Deploying to bioc_devel from @ db10177 🚀

data-representation.html

@@ -1597,7 +1597,7 @@ <h1 class="title">
 <div class="cell" data-layout-align="center" data-hash="data-representation_cache/html/unnamed-chunk-48_613feb304332cb6098ea31ae538c0ff9">
 <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">##  "/github/home/.cache/R/ExperimentHub/1bd812758271_7752"</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<span><span class="co">##  "/github/home/.cache/R/ExperimentHub/1a594277bd62_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" data-hash="data-representation_cache/html/unnamed-chunk-49_07b0f603f324c3454818c1410cb3cd50">
@@ -1667,15 +1667,15 @@ <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: /github/home/.cache/R/ExperimentHub/1bd812758271_7752 </span></span>
+<span><span class="co">##  .mcool file: /github/home/.cache/R/ExperimentHub/1a594277bd62_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: /github/home/.cache/R/ExperimentHub/1bd81b45cec6_7836 </span></span>
+<span><span class="co">##  .hic file: /github/home/.cache/R/ExperimentHub/1a5939a379f0_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>
@@ -1684,16 +1684,16 @@ <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:   /github/home/.cache/R/ExperimentHub/1bd837f28fd_7837 </span></span>
-<span><span class="co">##    $ regions:  /github/home/.cache/R/ExperimentHub/1bd873436f4_7838 </span></span>
+<span><span class="co">##    $ matrix:   /github/home/.cache/R/ExperimentHub/1a59dc812a9_7837 </span></span>
+<span><span class="co">##    $ regions:  /github/home/.cache/R/ExperimentHub/1a591fa0216e_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: /github/home/.cache/R/ExperimentHub/1bd86936f1c1_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/1a594e4de0cf_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>
@@ -1709,7 +1709,7 @@ <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: /github/home/.cache/R/ExperimentHub/1bd812758271_7752 </span></span>
+<span><span class="co">##  .mcool file: /github/home/.cache/R/ExperimentHub/1a594277bd62_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>
@@ -1807,7 +1807,7 @@ <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: "/github/home/.cache/R/ExperimentHub/1bd812758271_7752" </span></span>
+<span><span class="co">##  fileName: "/github/home/.cache/R/ExperimentHub/1a594277bd62_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>
@@ -1849,7 +1849,7 @@ <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" data-hash="data-representation_cache/html/unnamed-chunk-55_d36ff2f24162a6a16470a5d1582c04d5">
 <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] "/github/home/.cache/R/ExperimentHub/1bd812758271_7752"</span></span>
+<span><span class="co">##  [1] "/github/home/.cache/R/ExperimentHub/1a594277bd62_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>
@@ -1928,7 +1928,7 @@ <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: "/github/home/.cache/R/ExperimentHub/1bd81b45cec6_7836" </span></span>
+<span><span class="co">##  fileName: "/github/home/.cache/R/ExperimentHub/1a5939a379f0_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>
@@ -2370,14 +2370,14 @@ <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: "/github/home/.cache/R/ExperimentHub/1bd812758271_7752" </span></span>
+<span><span class="co">##  fileName: "/github/home/.cache/R/ExperimentHub/1a594277bd62_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: /github/home/.cache/R/ExperimentHub/1bd86936f1c1_7753 </span></span>
+<span><span class="co">##  pairsFile: /github/home/.cache/R/ExperimentHub/1a594e4de0cf_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">
@@ -2689,10 +2689,12 @@ <h1 class="title">
 </section><section id="pairsfile" class="level4" data-number="2.4.2.5"><h4 data-number="2.4.2.5" class="anchored" data-anchor-id="pairsfile">
 <span class="header-section-number">2.4.2.5</span> pairsFile</h4>
 <p>As a contact matrix is typically obtained from binning a <code>.pairs</code> file, it is often the case that the matching <code>.pairs</code> file is available to then end-user. A <code>PairsFile</code> can thus be created and associated to the corresponding <code>HiCExperiment</code> object. This allows more accurate estimation of contact distribution, e.g.&nbsp;when calculating distance-dependent genomic interaction frequency.</p>
-<div class="cell" data-layout-align="center" data-hash="data-representation_cache/html/unnamed-chunk-71_e4727f0a32e93787e558039374672bc5">
-<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>
+<div class="cell" data-layout-align="center" data-hash="data-representation_cache/html/unnamed-chunk-71_9ae43dd63b810a2a2b7dcc5ec8ebaa03">
+<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">##  "/github/home/.cache/R/ExperimentHub/1bd86936f1c1_7753"</span></span>
+<span><span class="co">##  "/github/home/.cache/R/ExperimentHub/1a594e4de0cf_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>

disseminating.html

@@ -484,7 +484,6 @@ <h1 class="title">
 </div>
 </section><section id="querying-a-complete-experiment-dataset" class="level3" data-number="8.1.2"><h3 data-number="8.1.2" class="anchored" data-anchor-id="querying-a-complete-experiment-dataset">
 <span class="header-section-number">8.1.2</span> Querying a complete experiment dataset</h3>
-<p>Rather than querying each genomic file independently, one can automatically fetch all the files associated with a given `experiment</p>
 <p>Rather than importing multiple files corresponding to a single experimentSet accession ID one by one, one can import all the available files associated with a experimentSet accession ID into a <code>HiCExperiment</code> object by using the <code><a href="https://rdrr.io/pkg/fourDNData/man/fourDNData.html">fourDNHiCExperiment()</a></code> function.</p>
 <div class="cell" data-layout-align="center" data-hash="disseminating_cache/html/unnamed-chunk-9_3eec30a0bd3579eafaff33086338a377">
 <div class="sourceCode" id="cb8"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="va">hic</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/fourDNData/man/fourDNData.html">fourDNHiCExperiment</a></span><span class="op">(</span><span class="st">'4DNESSS7VU57'</span><span class="op">)</span></span>