r1&quot;, ranges = IRanges(start = 1:10, width = 3))
rl &lt;- coverage(gr)
rl</code></pre>
<pre><code>## RleList of length 1
## $chr1
## integer-Rle of length 12 with 5 runs
##   Lengths: 1 1 8 1 1
##   Values : 1 2 3 2 1</code></pre>
<p>Let us consider a <code>GRanges</code> which we want to use to index into the <code>Rle</code>:</p>
<pre class="r"><code>grView &lt;- GRanges(&quot;chr1&quot;, ranges = IRanges(start = c(2,5), end = c(3,6)))</code></pre>
<p>We can subset directly into the <code>Rle</code> b