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date Sun, 03 Dec 2023 12:51:54 +0000
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<p><head>
<title>RBPBench - Motif Search Comparison Report</title></p>
<script src="/home/malong/miniconda3/envs/rbpbench/lib/python3.9/site-packages/rbpbench/content/sorttable.js" type="text/javascript"></script>
<p></head></p>
<h1>Comparison Report</h1>
<p>List of available comparison statistics generated
by RBPBench (rbpbench compare):</p>
<ul>
<li><a href="#method-tab-1">k562_eclip,human_v0.1,PUM1 method comparison table</a></li>
<li><a href="#method-tab-2">k562_eclip,human_v0.1,PUM2 method comparison table</a></li>
<li><a href="#method-venn-1">k562_eclip,human_v0.1,PUM1 method comparison plot</a></li>
<li><a href="#method-venn-2">k562_eclip,human_v0.1,PUM2 method comparison plot</a></li>
</ul>
<p>&nbsp;</p>
<h2 id="method-tab-1">k562_eclip,human_v0.1,PUM1 method comparison statistics</h2>
<p><strong>Table:</strong> RBP motif hit statistics for combined ID "k562_eclip,human_v0.1,PUM1" (data ID, motif database ID, RBP ID) over different methods (method ID column).</p>
<table class="sortable">
<thead>
<tr>
<th style="text-align: center;">Method ID</th>
<th style="text-align: center;"># regions</th>
<th style="text-align: center;"># motif hits</th>
<th style="text-align: center;">% regions with motifs</th>
<th style="text-align: center;">% motif nucleotides</th>
<th style="text-align: center;"># motif hits per 1000 nt</th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align: center;">dewseq_w100_s5</td>
<td style="text-align: center;">23</td>
<td style="text-align: center;">24</td>
<td style="text-align: center;">43.48</td>
<td style="text-align: center;">3.20</td>
<td style="text-align: center;">4.86</td>
</tr>
<tr>
<td style="text-align: center;">clipper_idr</td>
<td style="text-align: center;">32</td>
<td style="text-align: center;">8</td>
<td style="text-align: center;">18.75</td>
<td style="text-align: center;">2.69</td>
<td style="text-align: center;">3.84</td>
</tr>
</tbody>
</table>
<p>&nbsp;
&nbsp;</p>
<p>Column IDs have the following meanings: <strong>Method ID</strong> -&gt; method ID set for dataset (typically peak calling method ID), <strong># regions</strong> -&gt; number of peak regions used for motif search, <strong># motif hits</strong> -&gt; number of unique motif hits in peak regions (removed double counts), <strong>% regions with motifs</strong> -&gt; percentage of peak regions with motif hits, <strong>% motif nucleotides</strong> -&gt; percentage of unique motif nucleotides over effective peak region size (overlapping regions merged), <strong># motif hits per 1000 nt</strong> -&gt; number of motif hits over 1000 nt of called peak region size (overlapping regions NOT merged).</p>
<h2 id="method-tab-2">k562_eclip,human_v0.1,PUM2 method comparison statistics</h2>
<p><strong>Table:</strong> RBP motif hit statistics for combined ID "k562_eclip,human_v0.1,PUM2" (data ID, motif database ID, RBP ID) over different methods (method ID column).</p>
<table class="sortable">
<thead>
<tr>
<th style="text-align: center;">Method ID</th>
<th style="text-align: center;"># regions</th>
<th style="text-align: center;"># motif hits</th>
<th style="text-align: center;">% regions with motifs</th>
<th style="text-align: center;">% motif nucleotides</th>
<th style="text-align: center;"># motif hits per 1000 nt</th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align: center;">dewseq_w100_s5</td>
<td style="text-align: center;">70</td>
<td style="text-align: center;">448</td>
<td style="text-align: center;">92.86</td>
<td style="text-align: center;">14.08</td>
<td style="text-align: center;">31.46</td>
</tr>
<tr>
<td style="text-align: center;">clipper_idr</td>
<td style="text-align: center;">77</td>
<td style="text-align: center;">219</td>
<td style="text-align: center;">76.62</td>
<td style="text-align: center;">17.64</td>
<td style="text-align: center;">46.89</td>
</tr>
</tbody>
</table>
<p>&nbsp;
&nbsp;</p>
<p>Column IDs have the following meanings: <strong>Method ID</strong> -&gt; method ID set for dataset (typically peak calling method ID), <strong># regions</strong> -&gt; number of peak regions used for motif search, <strong># motif hits</strong> -&gt; number of unique motif hits in peak regions (removed double counts), <strong>% regions with motifs</strong> -&gt; percentage of peak regions with motif hits, <strong>% motif nucleotides</strong> -&gt; percentage of unique motif nucleotides over effective peak region size (overlapping regions merged), <strong># motif hits per 1000 nt</strong> -&gt; number of motif hits over 1000 nt of called peak region size (overlapping regions NOT merged).</p>
<h2 id="method-venn-1">k562_eclip,human_v0.1,PUM1 method comparison plot</h2>
<p>Based on the same combined ID "k562_eclip,human_v0.1,PUM1" (data ID, motif database ID, RBP ID), motif hit occurrences for 2 different methods (clipper_idr,dewseq_w100_s5) are compared via Venn diagram.
Any given motif hit can either be found only by one method, or be identified by any set (&gt;=2) of methods (intersection areas).</p>
<p><img src="html_report_plots/venn_diagram.method_comp.k562_eclip,human_v0.1,PUM1.png" alt="dataset comparison plot k562_eclip,human_v0.1,PUM1
title="dataset comparison plot k562_eclip,human_v0.1,PUM1" width="700" /></p>
<p><strong>Figure:</strong> Venn diagram of motif hit occurrences for 2 different methods (clipper_idr,dewseq_w100_s5) with identical combined ID (k562_eclip,human_v0.1,PUM1) + corresponding percentages of total motif hits for each region (method exclusive and intersection(s)).</p>
<p>&nbsp;</p>
<h2 id="method-venn-2">k562_eclip,human_v0.1,PUM2 method comparison plot</h2>
<p>Based on the same combined ID "k562_eclip,human_v0.1,PUM2" (data ID, motif database ID, RBP ID), motif hit occurrences for 2 different methods (clipper_idr,dewseq_w100_s5) are compared via Venn diagram.
Any given motif hit can either be found only by one method, or be identified by any set (&gt;=2) of methods (intersection areas).</p>
<p><img src="html_report_plots/venn_diagram.method_comp.k562_eclip,human_v0.1,PUM2.png" alt="dataset comparison plot k562_eclip,human_v0.1,PUM2
title="dataset comparison plot k562_eclip,human_v0.1,PUM2" width="700" /></p>
<p><strong>Figure:</strong> Venn diagram of motif hit occurrences for 2 different methods (clipper_idr,dewseq_w100_s5) with identical combined ID (k562_eclip,human_v0.1,PUM2) + corresponding percentages of total motif hits for each region (method exclusive and intersection(s)).</p>
<p>&nbsp;</p>