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python_api/dataset/l2g_prediction/index.html

@@ -2591,7 +2591,11 @@ <h2 id="otg.dataset.l2g_prediction.L2GPrediction" class="doc doc-heading">
 <span class="normal">82</span>
 <span class="normal">83</span>
 <span class="normal">84</span>
-<span class="normal">85</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@dataclass</span>
+<span class="normal">85</span>
+<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="nd">@dataclass</span>
 <span class="k">class</span> <span class="nc">L2GPrediction</span><span class="p">(</span><span class="n">Dataset</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Dataset that contains the Locus to Gene predictions.</span>
 
@@ -2613,6 +2617,7 @@ <h2 id="otg.dataset.l2g_prediction.L2GPrediction" class="doc doc-heading">
     <span class="k">def</span> <span class="nf">from_credible_set</span><span class="p">(</span>
         <span class="bp">cls</span><span class="p">:</span> <span class="n">Type</span><span class="p">[</span><span class="n">L2GPrediction</span><span class="p">],</span>
         <span class="n">model_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+        <span class="n">features_list</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span>
         <span class="n">study_locus</span><span class="p">:</span> <span class="n">StudyLocus</span><span class="p">,</span>
         <span class="n">study_index</span><span class="p">:</span> <span class="n">StudyIndex</span><span class="p">,</span>
         <span class="n">v2g</span><span class="p">:</span> <span class="n">V2G</span><span class="p">,</span>
@@ -2622,6 +2627,7 @@ <h2 id="otg.dataset.l2g_prediction.L2GPrediction" class="doc doc-heading">
 
 <span class="sd">        Args:</span>
 <span class="sd">            model_path (str): Path to the fitted model</span>
+<span class="sd">            features_list (list[str]): List of features to use for the model</span>
 <span class="sd">            study_locus (StudyLocus): Study locus dataset</span>
 <span class="sd">            study_index (StudyIndex): Study index dataset</span>
 <span class="sd">            v2g (V2G): Variant to gene dataset</span>
@@ -2630,6 +2636,7 @@ <h2 id="otg.dataset.l2g_prediction.L2GPrediction" class="doc doc-heading">
 <span class="sd">            L2GPrediction: L2G dataset</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="n">fm</span> <span class="o">=</span> <span class="n">L2GFeatureMatrix</span><span class="o">.</span><span class="n">generate_features</span><span class="p">(</span>
+            <span class="n">features_list</span><span class="o">=</span><span class="n">features_list</span><span class="p">,</span>
             <span class="n">study_locus</span><span class="o">=</span><span class="n">study_locus</span><span class="p">,</span>
             <span class="n">study_index</span><span class="o">=</span><span class="n">study_index</span><span class="p">,</span>
             <span class="n">variant_gene</span><span class="o">=</span><span class="n">v2g</span><span class="p">,</span>
@@ -2640,8 +2647,9 @@ <h2 id="otg.dataset.l2g_prediction.L2GPrediction" class="doc doc-heading">
             <span class="n">_df</span><span class="o">=</span><span class="p">(</span>
                 <span class="n">LocusToGeneModel</span><span class="o">.</span><span class="n">load_from_disk</span><span class="p">(</span>
                     <span class="n">model_path</span><span class="p">,</span>
-                    <span class="n">features_list</span><span class="o">=</span><span class="n">fm</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">drop</span><span class="p">(</span><span class="s2">&quot;studyLocusId&quot;</span><span class="p">,</span> <span class="s2">&quot;geneId&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">columns</span><span class="p">,</span>
-                <span class="p">)</span><span class="o">.</span><span class="n">predict</span><span class="p">(</span><span class="n">fm</span><span class="p">)</span>
+                    <span class="n">features_list</span><span class="o">=</span><span class="n">features_list</span><span class="p">,</span>
+                <span class="p">)</span>
+                <span class="o">.</span><span class="n">predict</span><span class="p">(</span><span class="n">fm</span><span class="p">)</span>
                 <span class="c1"># the probability of the positive class is the second element inside the probability array</span>
                 <span class="c1"># - this is selected as the L2G probability</span>
                 <span class="o">.</span><span class="n">select</span><span class="p">(</span>
@@ -2674,7 +2682,7 @@ <h2 id="otg.dataset.l2g_prediction.L2GPrediction" class="doc doc-heading">
 
 
 <h3 id="otg.dataset.l2g_prediction.L2GPrediction.from_credible_set" class="doc doc-heading">
-          <code class="highlight language-python"><span class="n">from_credible_set</span><span class="p">(</span><span class="n">model_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">study_locus</span><span class="p">:</span> <span class="n">StudyLocus</span><span class="p">,</span> <span class="n">study_index</span><span class="p">:</span> <span class="n">StudyIndex</span><span class="p">,</span> <span class="n">v2g</span><span class="p">:</span> <span class="n">V2G</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">L2GPrediction</span></code>
+          <code class="highlight language-python"><span class="n">from_credible_set</span><span class="p">(</span><span class="n">model_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">features_list</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span> <span class="n">study_locus</span><span class="p">:</span> <span class="n">StudyLocus</span><span class="p">,</span> <span class="n">study_index</span><span class="p">:</span> <span class="n">StudyIndex</span><span class="p">,</span> <span class="n">v2g</span><span class="p">:</span> <span class="n">V2G</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">L2GPrediction</span></code>
 
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small>
@@ -2714,6 +2722,20 @@ <h3 id="otg.dataset.l2g_prediction.L2GPrediction.from_credible_set" class="doc d
               <em>required</em>
           </td>
         </tr>
+        <tr>
+          <td><code>features_list</code></td>
+          <td>
+                <code>list[str]</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>List of features to use for the model</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
         <tr>
           <td><code>study_locus</code></td>
           <td>
@@ -2827,10 +2849,15 @@ <h3 id="otg.dataset.l2g_prediction.L2GPrediction.from_credible_set" class="doc d
 <span class="normal">82</span>
 <span class="normal">83</span>
 <span class="normal">84</span>
-<span class="normal">85</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@classmethod</span>
+<span class="normal">85</span>
+<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="nd">@classmethod</span>
 <span class="k">def</span> <span class="nf">from_credible_set</span><span class="p">(</span>
     <span class="bp">cls</span><span class="p">:</span> <span class="n">Type</span><span class="p">[</span><span class="n">L2GPrediction</span><span class="p">],</span>
     <span class="n">model_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+    <span class="n">features_list</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span>
     <span class="n">study_locus</span><span class="p">:</span> <span class="n">StudyLocus</span><span class="p">,</span>
     <span class="n">study_index</span><span class="p">:</span> <span class="n">StudyIndex</span><span class="p">,</span>
     <span class="n">v2g</span><span class="p">:</span> <span class="n">V2G</span><span class="p">,</span>
@@ -2840,6 +2867,7 @@ <h3 id="otg.dataset.l2g_prediction.L2GPrediction.from_credible_set" class="doc d
 
 <span class="sd">    Args:</span>
 <span class="sd">        model_path (str): Path to the fitted model</span>
+<span class="sd">        features_list (list[str]): List of features to use for the model</span>
 <span class="sd">        study_locus (StudyLocus): Study locus dataset</span>
 <span class="sd">        study_index (StudyIndex): Study index dataset</span>
 <span class="sd">        v2g (V2G): Variant to gene dataset</span>
@@ -2848,6 +2876,7 @@ <h3 id="otg.dataset.l2g_prediction.L2GPrediction.from_credible_set" class="doc d
 <span class="sd">        L2GPrediction: L2G dataset</span>
 <span class="sd">    &quot;&quot;&quot;</span>
     <span class="n">fm</span> <span class="o">=</span> <span class="n">L2GFeatureMatrix</span><span class="o">.</span><span class="n">generate_features</span><span class="p">(</span>
+        <span class="n">features_list</span><span class="o">=</span><span class="n">features_list</span><span class="p">,</span>
         <span class="n">study_locus</span><span class="o">=</span><span class="n">study_locus</span><span class="p">,</span>
         <span class="n">study_index</span><span class="o">=</span><span class="n">study_index</span><span class="p">,</span>
         <span class="n">variant_gene</span><span class="o">=</span><span class="n">v2g</span><span class="p">,</span>
@@ -2858,8 +2887,9 @@ <h3 id="otg.dataset.l2g_prediction.L2GPrediction.from_credible_set" class="doc d
         <span class="n">_df</span><span class="o">=</span><span class="p">(</span>
             <span class="n">LocusToGeneModel</span><span class="o">.</span><span class="n">load_from_disk</span><span class="p">(</span>
                 <span class="n">model_path</span><span class="p">,</span>
-                <span class="n">features_list</span><span class="o">=</span><span class="n">fm</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">drop</span><span class="p">(</span><span class="s2">&quot;studyLocusId&quot;</span><span class="p">,</span> <span class="s2">&quot;geneId&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">columns</span><span class="p">,</span>
-            <span class="p">)</span><span class="o">.</span><span class="n">predict</span><span class="p">(</span><span class="n">fm</span><span class="p">)</span>
+                <span class="n">features_list</span><span class="o">=</span><span class="n">features_list</span><span class="p">,</span>
+            <span class="p">)</span>
+            <span class="o">.</span><span class="n">predict</span><span class="p">(</span><span class="n">fm</span><span class="p">)</span>
             <span class="c1"># the probability of the positive class is the second element inside the probability array</span>
             <span class="c1"># - this is selected as the L2G probability</span>
             <span class="o">.</span><span class="n">select</span><span class="p">(</span>

python_api/datasource/finngen/_finngen/index.html

@@ -2381,6 +2381,8 @@ <h1>Finngen</h1>
     display: none;
   }
 </style>
+
+<p>FinnGen is a research project in genomics and personalized medicine. It is large public-private partnership that has collected and analysed genome and health data from 500,000 Finnish biobank donors to understand the genetic basis of diseases. FinnGen is a now expanding into understanding the progression and biological mechanisms of diseases. FinnGen provides a world-class resource for further breakthroughs in disease prevention, diagnosis, and treatment and a outlook into our genetic make-up.</p>
 <hr />
 <div class="md-source-file">
   <small>
@@ -2403,7 +2405,7 @@ <h1>Finngen</h1>
         <span class="icon twemoji">
           <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M21 13.1c-.1 0-.3.1-.4.2l-1 1 2.1 2.1 1-1c.2-.2.2-.6 0-.8l-1.3-1.3c-.1-.1-.2-.2-.4-.2m-1.9 1.8-6.1 6V23h2.1l6.1-6.1-2.1-2M12.5 7v5.2l4 2.4-1 1L11 13V7h1.5M11 21.9c-5.1-.5-9-4.8-9-9.9C2 6.5 6.5 2 12 2c5.3 0 9.6 4.1 10 9.3-.3-.1-.6-.2-1-.2s-.7.1-1 .2C19.6 7.2 16.2 4 12 4c-4.4 0-8 3.6-8 8 0 4.1 3.1 7.5 7.1 7.9l-.1.2v1.8Z"/></svg>
         </span>
-        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2023-10-31T12:33:26+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2023-10-31</span> </span>
+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2023-12-14T15:17:33+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2023-12-14</span> </span>
       </li>
 
 
@@ -2415,6 +2417,14 @@ <h1>Finngen</h1>
       </li>
       <li class="contributors-holder">
         <ul class="contributors" data-bi-name="contributors"><li>
+            <a
+              href="https://github.com/addramir"
+              title="addramir"
+              data-bi-name="contributorprofile"
+              target="_blank"
+              ><img src="https://avatars.githubusercontent.com/u/22906976?v=4" alt="addramir"
+            /></a>
+          </li><li>
             <a
               href="https://github.com/d0choa"
               title="d0choa"

python_api/method/l2g/_l2g/index.html

@@ -2406,15 +2406,7 @@ <h1>L2g</h1>
         <span class="label"> Contributors </span>
       </li>
       <li class="contributors-holder">
-        <ul class="contributors" data-bi-name="contributors"><li>
-            <a
-              href="https://github.com/ireneisdoomed"
-              title="ireneisdoomed"
-              data-bi-name="contributorprofile"
-              target="_blank"
-              ><img src="https://avatars.githubusercontent.com/u/45119610?v=4" alt="ireneisdoomed"
-            /></a>
-          </li></ul>
+        <ul class="contributors" data-bi-name="contributors"></ul>
       </li>
     </ul>
   </small>

python_api/method/l2g/evaluator/index.html

@@ -3382,15 +3382,7 @@ <h3 id="otg.method.l2g.evaluator.WandbEvaluator.setspark_ml_evaluator" class="do
         <span class="label"> Contributors </span>
       </li>
       <li class="contributors-holder">
-        <ul class="contributors" data-bi-name="contributors"><li>
-            <a
-              href="https://github.com/ireneisdoomed"
-              title="ireneisdoomed"
-              data-bi-name="contributorprofile"
-              target="_blank"
-              ><img src="https://avatars.githubusercontent.com/u/45119610?v=4" alt="ireneisdoomed"
-            /></a>
-          </li></ul>
+        <ul class="contributors" data-bi-name="contributors"></ul>
       </li>
     </ul>
   </small>

python_api/method/l2g/feature_factory/index.html

@@ -2995,23 +2995,7 @@ <h2 id="otg.method.l2g.feature_factory.StudyLocusFactory" class="doc doc-heading
         <span class="label"> Contributors </span>
       </li>
       <li class="contributors-holder">
-        <ul class="contributors" data-bi-name="contributors"><li>
-            <a
-              href="https://github.com/d0choa"
-              title="d0choa"
-              data-bi-name="contributorprofile"
-              target="_blank"
-              ><img src="https://avatars.githubusercontent.com/u/5097586?v=4" alt="d0choa"
-            /></a>
-          </li><li>
-            <a
-              href="https://github.com/ireneisdoomed"
-              title="ireneisdoomed"
-              data-bi-name="contributorprofile"
-              target="_blank"
-              ><img src="https://avatars.githubusercontent.com/u/45119610?v=4" alt="ireneisdoomed"
-            /></a>
-          </li></ul>
+        <ul class="contributors" data-bi-name="contributors"></ul>
       </li>
     </ul>
   </small>