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matrix-centric.html

@@ -381,7 +381,7 @@ <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>
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@@ -399,13 +399,13 @@ <h1 class="title">
 <section id="balancing-a-raw-interaction-count-map" class="level3 page-columns page-full" data-number="5.1.1"><h3 data-number="5.1.1" class="anchored" data-anchor-id="balancing-a-raw-interaction-count-map">
 <span class="header-section-number">5.1.1</span> Balancing a raw interaction count map</h3>
 <p>Hi-C sequencing coverage is systematically affected by multiple confounding factors, e.g.&nbsp; density of restriction sites, GC%, genome mappability, etc.. Overall, it generally ends up not homogenous throughout the entire genome and this leads to artifacts in un-normalized <code>count</code> matrices.</p>
-<p>To correct for sequencing coverage heterogeneity of raw <code>count</code> maps, Hi-C data can be normalized using matrix balancing approaches (<span class="citation" data-cites="Cournac_2012">Cournac et al. (<a href="interoperability.html#ref-Cournac_2012" role="doc-biblioref">2012</a>)</span>, <span class="citation" data-cites="Imakaev_2012">Imakaev et al. (<a href="interoperability.html#ref-Imakaev_2012" role="doc-biblioref">2012</a>)</span>). This is generally done directly on the disk-stored matrices using out-of-memory strategies (e.g.&nbsp;with <code>cooler balance &lt;.cool&gt;</code>). However, if contact matrix files are imported into a <code>HiCExperiment</code> object but no <code>balanced</code> scores are available, in-memory balancing can be performed using the <code>normalize</code> function.</p>
+<p>To correct for sequencing coverage heterogeneity of raw <code>count</code> maps, Hi-C data can be normalized using matrix balancing approaches (<span class="citation" data-cites="Cournac_2012">Cournac et al. (<a href="interoperability.html#ref-Cournac_2012" role="doc-biblioref">2012</a>)</span>, <span class="citation" data-cites="Imakaev_2012">Imakaev et al. (<a href="interoperability.html#ref-Imakaev_2012" role="doc-biblioref">2012</a>)</span>). This is generally done directly on the disk-stored matrices using out-of-memory strategies (e.g.&nbsp;with <code>cooler balance &lt;.cool&gt;</code>). However, if contact matrix files are imported into a <code>HiCExperiment</code> object but no <code>balanced</code> scores are available, in-memory balancing can be performed using the <code>normalize</code> function. This adds an extra <code>ICE</code> element in <code>scores</code> list (while the <code>interactions</code> themselves are unmodified).</p>
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 <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="va">normalized_hic</span> <span class="op">&lt;-</span> <span class="fu">normalize</span><span class="op">(</span><span class="va">hic</span><span class="op">)</span></span>
 <span><span class="va">normalized_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/1a9a4dc30249_7752" </span></span>
+<span><span class="co">##  fileName: "/github/home/.cache/R/ExperimentHub/1a92248c093f_7752" </span></span>
 <span><span class="co">##  focus: "II" </span></span>
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@@ -415,19 +415,6 @@ <h1 class="title">
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-<p>The only change done to the <code>HiCExperiment</code> object by the <code>normalize</code> function is the addition of a single extra <code>ICE</code> in <code>scores</code> list. The <code>interactions</code> themselves are unmodified.</p>
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 <p>It is possible to plot the different <code>scores</code> of the resulting object to visualize the newly computed <code>scores</code>. In this example, <code>ICE</code> scores should be nearly identical to <code>balanced</code> scores, which were originally imported from the disk-stored contact matrix.</p>
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@@ -449,13 +436,13 @@ <h1 class="title">
 <span class="header-section-number">5.1.2</span> Computing observed/expected (O/E) map</h3>
 <p>The most prominent feature of a balanced Hi-C matrix is the strong main diagonal. This main diagonal is observed because interactions between immediate adjacent genomic loci are more prone to happen than interactions spanning longer genomic distances. This “expected” behavior is due to the polymer nature of the chromosomes being studied, and can be locally estimated using the distance-dependent interaction frequency (a.k.a. the “distance law”, or P(s)). It can be used to compute an <code>expected</code> matrix on interactions.</p>
 <p>When it is desirable to “mask” this polymer behavior to emphasize topological structures formed by chromosomes, one can divide a given balanced matrix by its <code>expected</code> matrix, i.e.&nbsp;calculate the observed/expected (O/E) map. This is sometimes called “detrending”, as it effectively removes the average polymer behavior from the balanced matrix.</p>
-<p>The <code>detrend</code> function performs this operation on a given <code>HiCExperiment</code> object.</p>
+<p>The <code>detrend</code> function performs this operation on a given <code>HiCExperiment</code> object. It adds two extra elements in <code>scores</code> list: <code>expected</code> and <code>detrended</code> metrics (while the <code>interactions</code> themselves are unmodified).</p>
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 <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="va">detrended_hic</span> <span class="op">&lt;-</span> <span class="fu">detrend</span><span class="op">(</span><span class="va">hic</span><span class="op">)</span></span>
 <span><span class="va">detrended_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/1a9a4dc30249_7752" </span></span>
+<span><span class="co">##  fileName: "/github/home/.cache/R/ExperimentHub/1a92248c093f_7752" </span></span>
 <span><span class="co">##  focus: "II" </span></span>
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 <span><span class="co">##  active resolution: 2000 </span></span>
@@ -465,24 +452,6 @@ <h1 class="title">
 <span><span class="co">##  pairsFile: N/A </span></span>
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-<p>The only change done to the <code>HiCExperiment</code> object by the <code>detrend</code> function is the addition of two extra <code>scores</code>:</p>
-<ol type="1">
-<li><code>expected</code></li>
-<li><code>detrended</code></li>
-</ol>
-<p>The <code>interactions</code> themselves are unmodified.</p>
-</div>
-</div>
 <p>Topological features will be visually more prominent in the O/E <code>detrended</code> Hi-C map.</p>
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@@ -528,7 +497,7 @@ <h1 class="title">
 <span><span class="va">autocorr_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/1a9a4dc30249_7752" </span></span>
+<span><span class="co">##  fileName: "/github/home/.cache/R/ExperimentHub/1a92248c093f_7752" </span></span>
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@@ -600,7 +569,7 @@ <h1 class="title">
 <span><span class="va">hic2</span></span>
 <span><span class="co">##  `HiCExperiment` object with 168,785 contacts over 150 regions </span></span>
 <span><span class="co">##  -------</span></span>
-<span><span class="co">##  fileName: "/github/home/.cache/R/ExperimentHub/1a9a4dc30249_7752" </span></span>
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 <span><span class="co">##  focus: "II:400,000-700,000" </span></span>
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 <span><span class="co">##  active resolution: 2000 </span></span>