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Author: ielis

stable/apidocs/gpsea.analysis.clf.html

@@ -282,7 +282,7 @@
 
 <dl class="py function">
 <dt class="sig sig-object py" id="gpsea.analysis.clf.diagnosis_classifier">
-<span class="sig-prename descclassname"><span class="pre">gpsea.analysis.clf.</span></span><span class="sig-name descname"><span class="pre">diagnosis_classifier</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">diagnoses</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Iterable" title="(in Python v3.14)"><span class="pre">Iterable</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.14)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://ielis.github.io/hpo-toolkit/stable/apidocs/hpotk.model.html#hpotk.model.TermId" title="(in hpo-toolkit)"><span class="pre">TermId</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">labels</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Iterable" title="(in Python v3.14)"><span class="pre">Iterable</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.14)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.14)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference internal" href="#gpsea.analysis.clf.GenotypeClassifier" title="gpsea.analysis.clf._api.GenotypeClassifier"><span class="pre">GenotypeClassifier</span></a></span></span><a class="reference internal" href="../_modules/gpsea/analysis/clf/_gt_classifiers.html#diagnosis_classifier"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.clf.diagnosis_classifier" title="Link to this definition"></a></dt>
+<span class="sig-prename descclassname"><span class="pre">gpsea.analysis.clf.</span></span><span class="sig-name descname"><span class="pre">diagnosis_classifier</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">diagnoses</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Iterable" title="(in Python v3.14)"><span class="pre">Iterable</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://ielis.github.io/hpo-toolkit/stable/apidocs/hpotk.model.html#hpotk.model.TermId" title="(in hpo-toolkit)"><span class="pre">TermId</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.14)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">labels</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Iterable" title="(in Python v3.14)"><span class="pre">Iterable</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.14)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.14)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference internal" href="#gpsea.analysis.clf.GenotypeClassifier" title="gpsea.analysis.clf._api.GenotypeClassifier"><span class="pre">GenotypeClassifier</span></a></span></span><a class="reference internal" href="../_modules/gpsea/analysis/clf/_gt_classifiers.html#diagnosis_classifier"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.clf.diagnosis_classifier" title="Link to this definition"></a></dt>
 <dd><p>Genotype classifier bins an individual based on presence of a disease diagnosis,
 as listed in <a class="reference internal" href="gpsea.model.html#gpsea.model.Patient.diseases" title="gpsea.model.Patient.diseases"><code class="xref py py-attr docutils literal notranslate"><span class="pre">diseases</span></code></a> attribute.</p>
 <p>If the individual is diagnosed with more than one disease from the provided <cite>diagnoses</cite>,

stable/apidocs/gpsea.analysis.mtc_filter.html

@@ -260,7 +260,7 @@
 
 <dl class="py class">
 <dt class="sig sig-object py" id="gpsea.analysis.mtc_filter.SpecifiedTermsMtcFilter">
-<span class="property"><span class="k"><span class="pre">class</span></span><span class="w"> </span></span><span class="sig-prename descclassname"><span class="pre">gpsea.analysis.mtc_filter.</span></span><span class="sig-name descname"><span class="pre">SpecifiedTermsMtcFilter</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">terms_to_test</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Iterable" title="(in Python v3.14)"><span class="pre">Iterable</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.14)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://ielis.github.io/hpo-toolkit/stable/apidocs/hpotk.model.html#hpotk.model.TermId" title="(in hpo-toolkit)"><span class="pre">TermId</span></a><span class="p"><span class="pre">]</span></span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/gpsea/analysis/mtc_filter/_impl.html#SpecifiedTermsMtcFilter"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.mtc_filter.SpecifiedTermsMtcFilter" title="Link to this definition"></a></dt>
+<span class="property"><span class="k"><span class="pre">class</span></span><span class="w"> </span></span><span class="sig-prename descclassname"><span class="pre">gpsea.analysis.mtc_filter.</span></span><span class="sig-name descname"><span class="pre">SpecifiedTermsMtcFilter</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">terms_to_test</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Iterable" title="(in Python v3.14)"><span class="pre">Iterable</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://ielis.github.io/hpo-toolkit/stable/apidocs/hpotk.model.html#hpotk.model.TermId" title="(in hpo-toolkit)"><span class="pre">TermId</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.14)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/gpsea/analysis/mtc_filter/_impl.html#SpecifiedTermsMtcFilter"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.mtc_filter.SpecifiedTermsMtcFilter" title="Link to this definition"></a></dt>
 <dd><p>Bases: <a class="reference internal" href="#gpsea.analysis.mtc_filter.PhenotypeMtcFilter" title="gpsea.analysis.mtc_filter._impl.PhenotypeMtcFilter"><code class="xref py py-class docutils literal notranslate"><span class="pre">PhenotypeMtcFilter</span></code></a>[<a class="reference external" href="https://ielis.github.io/hpo-toolkit/stable/apidocs/hpotk.model.html#hpotk.model.TermId" title="(in hpo-toolkit)"><code class="xref py py-class docutils literal notranslate"><span class="pre">TermId</span></code></a>]</p>
 <p><cite>SpecifiedTermsMtcFilter</cite> limits the HPO terms to be tested to a selection of provided terms.</p>
 <p>In cases where we have a hypothesis about which phenotypes are relevant for

stable/apidocs/gpsea.analysis.pscore.html

@@ -253,7 +253,7 @@
 This predicate is intended to be used with the Mann Whitney U test.</p>
 <dl class="py method">
 <dt class="sig sig-object py" id="gpsea.analysis.pscore.CountingPhenotypeScorer.from_query_curies">
-<span class="property"><span class="k"><span class="pre">static</span></span><span class="w"> </span></span><span class="sig-name descname"><span class="pre">from_query_curies</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">hpo</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://ielis.github.io/hpo-toolkit/stable/apidocs/hpotk.ontology.html#hpotk.ontology.MinimalOntology" title="(in hpo-toolkit)"><span class="pre">MinimalOntology</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">query</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Iterable" title="(in Python v3.14)"><span class="pre">Iterable</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.14)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://ielis.github.io/hpo-toolkit/stable/apidocs/hpotk.model.html#hpotk.model.TermId" title="(in hpo-toolkit)"><span class="pre">TermId</span></a><span class="p"><span class="pre">]</span></span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/gpsea/analysis/pscore/_hpo.html#CountingPhenotypeScorer.from_query_curies"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.pscore.CountingPhenotypeScorer.from_query_curies" title="Link to this definition"></a></dt>
+<span class="property"><span class="k"><span class="pre">static</span></span><span class="w"> </span></span><span class="sig-name descname"><span class="pre">from_query_curies</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">hpo</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://ielis.github.io/hpo-toolkit/stable/apidocs/hpotk.ontology.html#hpotk.ontology.MinimalOntology" title="(in hpo-toolkit)"><span class="pre">MinimalOntology</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">query</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Iterable" title="(in Python v3.14)"><span class="pre">Iterable</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://ielis.github.io/hpo-toolkit/stable/apidocs/hpotk.model.html#hpotk.model.TermId" title="(in hpo-toolkit)"><span class="pre">TermId</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.14)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/gpsea/analysis/pscore/_hpo.html#CountingPhenotypeScorer.from_query_curies"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gpsea.analysis.pscore.CountingPhenotypeScorer.from_query_curies" title="Link to this definition"></a></dt>
 <dd><p>Create a scorer to test for the number of phenotype terms that fall into the phenotype groups.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>