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opentargets · Oct 13, 2023 · 9a959a7 · 9a959a7
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diff --git a/components/dataset/_dataset/index.html b/components/dataset/_dataset/index.html
@@ -239,7 +239,7 @@
     <span class=n>schema</span> <span class=o>=</span> <span class=bp>cls</span><span class=o>.</span><span class=n>get_schema</span><span class=p>()</span>
     <span class=n>df</span> <span class=o>=</span> <span class=n>session</span><span class=o>.</span><span class=n>read_parquet</span><span class=p>(</span><span class=n>path</span><span class=o>=</span><span class=n>path</span><span class=p>,</span> <span class=n>schema</span><span class=o>=</span><span class=n>schema</span><span class=p>,</span> <span class=o>**</span><span class=n>kwargs</span><span class=p>)</span>
     <span class=k>return</span> <span class=bp>cls</span><span class=p>(</span><span class=n>_df</span><span class=o>=</span><span class=n>df</span><span class=p>,</span> <span class=n>_schema</span><span class=o>=</span><span class=n>schema</span><span class=p>)</span>
-</code></pre></div></td></tr></table></div> </details> </div> </div> <div class="doc doc-object doc-function"> <h2 id=otg.dataset.dataset.Dataset.get_schema class="doc doc-heading"> <code class="highlight language-python"><span class=n>get_schema</span><span class=p>()</span></code> <span class="doc doc-labels"> <small class="doc doc-label doc-label-abstractmethod"><code>abstractmethod</code></small> <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small> </span> </h2> <div class="doc doc-contents "> <p>Abstract method to get the schema. Must be implemented by child classes.</p> <details class=quote> <summary>Source code in <code>src/otg/dataset/dataset.py</code></summary> <div class=highlight><table class=highlighttable><tr><td class=linenos><div class=linenodiv><pre><span></span><span class=normal>47</span>
+</code></pre></div></td></tr></table></div> </details> </div> </div> <div class="doc doc-object doc-function"> <h2 id=otg.dataset.dataset.Dataset.get_schema class="doc doc-heading"> <code class="highlight language-python"><span class=n>get_schema</span><span class=p>()</span></code> <span class="doc doc-labels"> <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small> <small class="doc doc-label doc-label-abstractmethod"><code>abstractmethod</code></small> </span> </h2> <div class="doc doc-contents "> <p>Abstract method to get the schema. Must be implemented by child classes.</p> <details class=quote> <summary>Source code in <code>src/otg/dataset/dataset.py</code></summary> <div class=highlight><table class=highlighttable><tr><td class=linenos><div class=linenodiv><pre><span></span><span class=normal>47</span>
 <span class=normal>48</span>
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diff --git a/components/dataset/summary_statistics/index.html b/components/dataset/summary_statistics/index.html
@@ -90,10 +90,7 @@
 <span class=normal>109</span>
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-<span class=normal>112</span>
-<span class=normal>113</span>
-<span class=normal>114</span>
-<span class=normal>115</span></pre></div></td><td class=code><div><pre><span></span><code><span class=nd>@dataclass</span>
+<span class=normal>112</span></pre></div></td><td class=code><div><pre><span></span><code><span class=nd>@dataclass</span>
 <span class=k>class</span> <span class=nc>SummaryStatistics</span><span class=p>(</span><span class=n>Dataset</span><span class=p>):</span>
 <span class=w>    </span><span class=sd>&quot;&quot;&quot;Summary Statistics dataset.</span>
 
@@ -131,7 +128,6 @@
         <span class=bp>self</span><span class=p>:</span> <span class=n>SummaryStatistics</span><span class=p>,</span>
         <span class=n>distance</span><span class=p>:</span> <span class=nb>int</span><span class=p>,</span>
         <span class=n>gwas_significance</span><span class=p>:</span> <span class=nb>float</span> <span class=o>=</span> <span class=mf>5e-8</span><span class=p>,</span>
-        <span class=n>with_locus</span><span class=p>:</span> <span class=nb>bool</span> <span class=o>=</span> <span class=kc>False</span><span class=p>,</span>
         <span class=n>baseline_significance</span><span class=p>:</span> <span class=nb>float</span> <span class=o>=</span> <span class=mf>0.05</span><span class=p>,</span>
         <span class=n>locus_collect_distance</span><span class=p>:</span> <span class=nb>int</span> <span class=o>|</span> <span class=kc>None</span> <span class=o>=</span> <span class=kc>None</span><span class=p>,</span>
     <span class=p>)</span> <span class=o>-&gt;</span> <span class=n>StudyLocus</span><span class=p>:</span>
@@ -146,10 +142,8 @@
 <span class=sd>        Returns:</span>
 <span class=sd>            StudyLocus: Clumped study-locus containing variants based on window.</span>
 <span class=sd>        &quot;&quot;&quot;</span>
-        <span class=k>if</span> <span class=n>locus_collect_distance</span> <span class=ow>is</span> <span class=kc>None</span><span class=p>:</span>
-            <span class=n>locus_collect_distance</span> <span class=o>=</span> <span class=n>distance</span>
-        <span class=c1># Based on if we want to get the locus different clumping function is called:</span>
-        <span class=k>if</span> <span class=n>with_locus</span><span class=p>:</span>
+        <span class=c1># If locus collect distance is present, collect locus with the provided distance:</span>
+        <span class=k>if</span> <span class=n>locus_collect_distance</span><span class=p>:</span>
             <span class=n>clumped_df</span> <span class=o>=</span> <span class=n>WindowBasedClumping</span><span class=o>.</span><span class=n>clump_with_locus</span><span class=p>(</span>
                 <span class=bp>self</span><span class=p>,</span>
                 <span class=n>window_length</span><span class=o>=</span><span class=n>distance</span><span class=p>,</span>
@@ -189,7 +183,10 @@
             <span class=p>),</span>
             <span class=n>_schema</span><span class=o>=</span><span class=n>SummaryStatistics</span><span class=o>.</span><span class=n>get_schema</span><span class=p>(),</span>
         <span class=p>)</span>
-</code></pre></div></td></tr></table></div> </details> <div class="doc doc-children"> <div class="doc doc-object doc-function"> <h2 id=otg.dataset.summary_statistics.SummaryStatistics.exclude_region class="doc doc-heading"> <code class="highlight language-python"><span class=n>exclude_region</span><span class=p>(</span><span class=n>region</span><span class=p>)</span></code> </h2> <div class="doc doc-contents "> <p>Exclude a region from the summary stats dataset.</p> <p><strong>Parameters:</strong></p> <table> <thead> <tr> <th>Name</th> <th>Type</th> <th>Description</th> <th>Default</th> </tr> </thead> <tbody> <tr> <td><code>region</code></td> <td> <code>str</code> </td> <td><p>region given in "chr##:#####-####" format</p></td> <td> <em>required</em> </td> </tr> </tbody> </table> <p><strong>Returns:</strong></p> <table> <thead> <tr> <th>Name</th> <th>Type</th> <th>Description</th> </tr> </thead> <tbody> <tr> <td><code>SummaryStatistics</code></td> <td> <code><a class="autorefs autorefs-internal" title="otg.dataset.summary_statistics.SummaryStatistics" href="#otg.dataset.summary_statistics.SummaryStatistics">SummaryStatistics</a></code> </td> <td><p>filtered summary statistics.</p></td> </tr> </tbody> </table> <details class=quote> <summary>Source code in <code>src/otg/dataset/summary_statistics.py</code></summary> <div class=highlight><table class=highlighttable><tr><td class=linenos><div class=linenodiv><pre><span></span><span class=normal> 91</span>
+</code></pre></div></td></tr></table></div> </details> <div class="doc doc-children"> <div class="doc doc-object doc-function"> <h2 id=otg.dataset.summary_statistics.SummaryStatistics.exclude_region class="doc doc-heading"> <code class="highlight language-python"><span class=n>exclude_region</span><span class=p>(</span><span class=n>region</span><span class=p>)</span></code> </h2> <div class="doc doc-contents "> <p>Exclude a region from the summary stats dataset.</p> <p><strong>Parameters:</strong></p> <table> <thead> <tr> <th>Name</th> <th>Type</th> <th>Description</th> <th>Default</th> </tr> </thead> <tbody> <tr> <td><code>region</code></td> <td> <code>str</code> </td> <td><p>region given in "chr##:#####-####" format</p></td> <td> <em>required</em> </td> </tr> </tbody> </table> <p><strong>Returns:</strong></p> <table> <thead> <tr> <th>Name</th> <th>Type</th> <th>Description</th> </tr> </thead> <tbody> <tr> <td><code>SummaryStatistics</code></td> <td> <code><a class="autorefs autorefs-internal" title="otg.dataset.summary_statistics.SummaryStatistics" href="#otg.dataset.summary_statistics.SummaryStatistics">SummaryStatistics</a></code> </td> <td><p>filtered summary statistics.</p></td> </tr> </tbody> </table> <details class=quote> <summary>Source code in <code>src/otg/dataset/summary_statistics.py</code></summary> <div class=highlight><table class=highlighttable><tr><td class=linenos><div class=linenodiv><pre><span></span><span class=normal> 88</span>
+<span class=normal> 89</span>
+<span class=normal> 90</span>
+<span class=normal> 91</span>
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@@ -210,10 +207,7 @@
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-<span class=normal>112</span>
-<span class=normal>113</span>
-<span class=normal>114</span>
-<span class=normal>115</span></pre></div></td><td class=code><div><pre><span></span><code><span class=k>def</span> <span class=nf>exclude_region</span><span class=p>(</span><span class=bp>self</span><span class=p>:</span> <span class=n>SummaryStatistics</span><span class=p>,</span> <span class=n>region</span><span class=p>:</span> <span class=nb>str</span><span class=p>)</span> <span class=o>-&gt;</span> <span class=n>SummaryStatistics</span><span class=p>:</span>
+<span class=normal>112</span></pre></div></td><td class=code><div><pre><span></span><code><span class=k>def</span> <span class=nf>exclude_region</span><span class=p>(</span><span class=bp>self</span><span class=p>:</span> <span class=n>SummaryStatistics</span><span class=p>,</span> <span class=n>region</span><span class=p>:</span> <span class=nb>str</span><span class=p>)</span> <span class=o>-&gt;</span> <span class=n>SummaryStatistics</span><span class=p>:</span>
 <span class=w>    </span><span class=sd>&quot;&quot;&quot;Exclude a region from the summary stats dataset.</span>
 
 <span class=sd>    Args:</span>
@@ -286,7 +280,7 @@
         <span class=p>)</span>
     <span class=p>)</span>
     <span class=k>return</span> <span class=n>SummaryStatistics</span><span class=p>(</span><span class=n>_df</span><span class=o>=</span><span class=n>df</span><span class=p>,</span> <span class=n>_schema</span><span class=o>=</span><span class=bp>self</span><span class=o>.</span><span class=n>_schema</span><span class=p>)</span>
-</code></pre></div></td></tr></table></div> </details> </div> </div> <div class="doc doc-object doc-function"> <h2 id=otg.dataset.summary_statistics.SummaryStatistics.window_based_clumping class="doc doc-heading"> <code class="highlight language-python"><span class=n>window_based_clumping</span><span class=p>(</span><span class=n>distance</span><span class=p>,</span> <span class=n>gwas_significance</span><span class=o>=</span><span class=mf>5e-08</span><span class=p>,</span> <span class=n>with_locus</span><span class=o>=</span><span class=kc>False</span><span class=p>,</span> <span class=n>baseline_significance</span><span class=o>=</span><span class=mf>0.05</span><span class=p>,</span> <span class=n>locus_collect_distance</span><span class=o>=</span><span class=kc>None</span><span class=p>)</span></code> </h2> <div class="doc doc-contents "> <p>Generate study-locus from summary statistics by distance based clumping + collect locus.</p> <p><strong>Parameters:</strong></p> <table> <thead> <tr> <th>Name</th> <th>Type</th> <th>Description</th> <th>Default</th> </tr> </thead> <tbody> <tr> <td><code>distance</code></td> <td> <code>int</code> </td> <td><p>Distance in base pairs to be used for clumping.</p></td> <td> <em>required</em> </td> </tr> <tr> <td><code>gwas_significance</code></td> <td> <code>float</code> </td> <td><p>GWAS significance threshold. Defaults to 5e-8.</p></td> <td> <code>5e-08</code> </td> </tr> <tr> <td><code>baseline_significance</code></td> <td> <code>float</code> </td> <td><p>Baseline significance threshold for inclusion in the locus. Defaults to 0.05.</p></td> <td> <code>0.05</code> </td> </tr> <tr> <td><code>locus_collect_distance</code></td> <td> <code>int</code> </td> <td><p>The distance to collect locus around semi-indices. If not provided, defaults to <code>distance</code>.</p></td> <td> <code>None</code> </td> </tr> </tbody> </table> <p><strong>Returns:</strong></p> <table> <thead> <tr> <th>Name</th> <th>Type</th> <th>Description</th> </tr> </thead> <tbody> <tr> <td><code>StudyLocus</code></td> <td> <code><a class="autorefs autorefs-internal" title="otg.dataset.study_locus.StudyLocus" href="../study_locus/#otg.dataset.study_locus.StudyLocus">StudyLocus</a></code> </td> <td><p>Clumped study-locus containing variants based on window.</p></td> </tr> </tbody> </table> <details class=quote> <summary>Source code in <code>src/otg/dataset/summary_statistics.py</code></summary> <div class=highlight><table class=highlighttable><tr><td class=linenos><div class=linenodiv><pre><span></span><span class=normal>54</span>
+</code></pre></div></td></tr></table></div> </details> </div> </div> <div class="doc doc-object doc-function"> <h2 id=otg.dataset.summary_statistics.SummaryStatistics.window_based_clumping class="doc doc-heading"> <code class="highlight language-python"><span class=n>window_based_clumping</span><span class=p>(</span><span class=n>distance</span><span class=p>,</span> <span class=n>gwas_significance</span><span class=o>=</span><span class=mf>5e-08</span><span class=p>,</span> <span class=n>baseline_significance</span><span class=o>=</span><span class=mf>0.05</span><span class=p>,</span> <span class=n>locus_collect_distance</span><span class=o>=</span><span class=kc>None</span><span class=p>)</span></code> </h2> <div class="doc doc-contents "> <p>Generate study-locus from summary statistics by distance based clumping + collect locus.</p> <p><strong>Parameters:</strong></p> <table> <thead> <tr> <th>Name</th> <th>Type</th> <th>Description</th> <th>Default</th> </tr> </thead> <tbody> <tr> <td><code>distance</code></td> <td> <code>int</code> </td> <td><p>Distance in base pairs to be used for clumping.</p></td> <td> <em>required</em> </td> </tr> <tr> <td><code>gwas_significance</code></td> <td> <code>float</code> </td> <td><p>GWAS significance threshold. Defaults to 5e-8.</p></td> <td> <code>5e-08</code> </td> </tr> <tr> <td><code>baseline_significance</code></td> <td> <code>float</code> </td> <td><p>Baseline significance threshold for inclusion in the locus. Defaults to 0.05.</p></td> <td> <code>0.05</code> </td> </tr> <tr> <td><code>locus_collect_distance</code></td> <td> <code>int</code> </td> <td><p>The distance to collect locus around semi-indices. If not provided, defaults to <code>distance</code>.</p></td> <td> <code>None</code> </td> </tr> </tbody> </table> <p><strong>Returns:</strong></p> <table> <thead> <tr> <th>Name</th> <th>Type</th> <th>Description</th> </tr> </thead> <tbody> <tr> <td><code>StudyLocus</code></td> <td> <code><a class="autorefs autorefs-internal" title="otg.dataset.study_locus.StudyLocus" href="../study_locus/#otg.dataset.study_locus.StudyLocus">StudyLocus</a></code> </td> <td><p>Clumped study-locus containing variants based on window.</p></td> </tr> </tbody> </table> <details class=quote> <summary>Source code in <code>src/otg/dataset/summary_statistics.py</code></summary> <div class=highlight><table class=highlighttable><tr><td class=linenos><div class=linenodiv><pre><span></span><span class=normal>54</span>
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@@ -318,14 +312,10 @@
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-<span class=normal>86</span>
-<span class=normal>87</span>
-<span class=normal>88</span>
-<span class=normal>89</span></pre></div></td><td class=code><div><pre><span></span><code><span class=k>def</span> <span class=nf>window_based_clumping</span><span class=p>(</span>
+<span class=normal>86</span></pre></div></td><td class=code><div><pre><span></span><code><span class=k>def</span> <span class=nf>window_based_clumping</span><span class=p>(</span>
     <span class=bp>self</span><span class=p>:</span> <span class=n>SummaryStatistics</span><span class=p>,</span>
     <span class=n>distance</span><span class=p>:</span> <span class=nb>int</span><span class=p>,</span>
     <span class=n>gwas_significance</span><span class=p>:</span> <span class=nb>float</span> <span class=o>=</span> <span class=mf>5e-8</span><span class=p>,</span>
-    <span class=n>with_locus</span><span class=p>:</span> <span class=nb>bool</span> <span class=o>=</span> <span class=kc>False</span><span class=p>,</span>
     <span class=n>baseline_significance</span><span class=p>:</span> <span class=nb>float</span> <span class=o>=</span> <span class=mf>0.05</span><span class=p>,</span>
     <span class=n>locus_collect_distance</span><span class=p>:</span> <span class=nb>int</span> <span class=o>|</span> <span class=kc>None</span> <span class=o>=</span> <span class=kc>None</span><span class=p>,</span>
 <span class=p>)</span> <span class=o>-&gt;</span> <span class=n>StudyLocus</span><span class=p>:</span>
@@ -340,10 +330,8 @@
 <span class=sd>    Returns:</span>
 <span class=sd>        StudyLocus: Clumped study-locus containing variants based on window.</span>
 <span class=sd>    &quot;&quot;&quot;</span>
-    <span class=k>if</span> <span class=n>locus_collect_distance</span> <span class=ow>is</span> <span class=kc>None</span><span class=p>:</span>
-        <span class=n>locus_collect_distance</span> <span class=o>=</span> <span class=n>distance</span>
-    <span class=c1># Based on if we want to get the locus different clumping function is called:</span>
-    <span class=k>if</span> <span class=n>with_locus</span><span class=p>:</span>
+    <span class=c1># If locus collect distance is present, collect locus with the provided distance:</span>
+    <span class=k>if</span> <span class=n>locus_collect_distance</span><span class=p>:</span>
         <span class=n>clumped_df</span> <span class=o>=</span> <span class=n>WindowBasedClumping</span><span class=o>.</span><span class=n>clump_with_locus</span><span class=p>(</span>
             <span class=bp>self</span><span class=p>,</span>
             <span class=n>window_length</span><span class=o>=</span><span class=n>distance</span><span class=p>,</span>

diff --git a/search/search_index.json b/search/search_index.json