Commit 92a461de authored by hjulienne's avatar hjulienne
Browse files

add filter imputation quality

parent 8f85b369
Pipeline #19045 passed with stages
in 57 seconds
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config: 7890896c7cf0d3614ade393a5c103246
config: f0cd103aab646a141229409df671f02e
tags: 645f666f9bcd5a90fca523b33c5a78b7
......@@ -17,32 +17,34 @@
<script type="text/javascript" src="../_static/js/modernizr.min.js"></script>
<script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
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<link rel="index" title="Index" href="../genindex.html" />
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<script src="../_static/js/modernizr.min.js"></script>
</head>
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......@@ -161,12 +163,12 @@
<span id="jass-preprocessing-compute-score-module"></span><h2>jass_preprocessing.compute_score module<a class="headerlink" href="#module-jass_preprocessing.compute_score" title="Permalink to this headline"></a></h2>
<dl class="function">
<dt id="jass_preprocessing.compute_score.compute_sample_size">
<code class="descclassname">jass_preprocessing.compute_score.</code><code class="descname">compute_sample_size</code><span class="sig-paren">(</span><em>mgwas</em>, <em>diagnostic_folder</em>, <em>trait</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/compute_score.html#compute_sample_size"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#jass_preprocessing.compute_score.compute_sample_size" title="Permalink to this definition"></a></dt>
<code class="sig-prename descclassname">jass_preprocessing.compute_score.</code><code class="sig-name descname">compute_sample_size</code><span class="sig-paren">(</span><em class="sig-param">mgwas</em>, <em class="sig-param">diagnostic_folder</em>, <em class="sig-param">trait</em>, <em class="sig-param">perSS=0.7</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/compute_score.html#compute_sample_size"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#jass_preprocessing.compute_score.compute_sample_size" title="Permalink to this definition"></a></dt>
<dd></dd></dl>
<dl class="function">
<dt id="jass_preprocessing.compute_score.compute_z_score">
<code class="descclassname">jass_preprocessing.compute_score.</code><code class="descname">compute_z_score</code><span class="sig-paren">(</span><em>mgwas</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/compute_score.html#compute_z_score"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#jass_preprocessing.compute_score.compute_z_score" title="Permalink to this definition"></a></dt>
<code class="sig-prename descclassname">jass_preprocessing.compute_score.</code><code class="sig-name descname">compute_z_score</code><span class="sig-paren">(</span><em class="sig-param">mgwas</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/compute_score.html#compute_z_score"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#jass_preprocessing.compute_score.compute_z_score" title="Permalink to this definition"></a></dt>
<dd><p>Compute zscore value and sign1
add the corresponding column to the mgwas dataframe</p>
</dd></dl>
......@@ -177,12 +179,12 @@ add the corresponding column to the mgwas dataframe</p>
<p>Few fonction to to compute DNA complement</p>
<dl class="function">
<dt id="jass_preprocessing.dna_utils.dna_complement">
<code class="descclassname">jass_preprocessing.dna_utils.</code><code class="descname">dna_complement</code><span class="sig-paren">(</span><em>input</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/dna_utils.html#dna_complement"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#jass_preprocessing.dna_utils.dna_complement" title="Permalink to this definition"></a></dt>
<code class="sig-prename descclassname">jass_preprocessing.dna_utils.</code><code class="sig-name descname">dna_complement</code><span class="sig-paren">(</span><em class="sig-param">input</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/dna_utils.html#dna_complement"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#jass_preprocessing.dna_utils.dna_complement" title="Permalink to this definition"></a></dt>
<dd></dd></dl>
<dl class="function">
<dt id="jass_preprocessing.dna_utils.dna_complement_base">
<code class="descclassname">jass_preprocessing.dna_utils.</code><code class="descname">dna_complement_base</code><span class="sig-paren">(</span><em>inputbase</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/dna_utils.html#dna_complement_base"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#jass_preprocessing.dna_utils.dna_complement_base" title="Permalink to this definition"></a></dt>
<code class="sig-prename descclassname">jass_preprocessing.dna_utils.</code><code class="sig-name descname">dna_complement_base</code><span class="sig-paren">(</span><em class="sig-param">inputbase</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/dna_utils.html#dna_complement_base"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#jass_preprocessing.dna_utils.dna_complement_base" title="Permalink to this definition"></a></dt>
<dd></dd></dl>
</div>
......@@ -193,102 +195,84 @@ add the corresponding column to the mgwas dataframe</p>
to map columns</p>
<dl class="function">
<dt id="jass_preprocessing.map_gwas.convert_missing_values">
<code class="descclassname">jass_preprocessing.map_gwas.</code><code class="descname">convert_missing_values</code><span class="sig-paren">(</span><em>df</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/map_gwas.html#convert_missing_values"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#jass_preprocessing.map_gwas.convert_missing_values" title="Permalink to this definition"></a></dt>
<code class="sig-prename descclassname">jass_preprocessing.map_gwas.</code><code class="sig-name descname">convert_missing_values</code><span class="sig-paren">(</span><em class="sig-param">df</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/map_gwas.html#convert_missing_values"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#jass_preprocessing.map_gwas.convert_missing_values" title="Permalink to this definition"></a></dt>
<dd><p>Convert all missing value strings to a standart np.nan value</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>GWAS_table</strong> (<em>pandas dataframe</em>) – GWAS data as a dataframe</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">a pandas dataframe with missing value all equal to np.nan</td>
</tr>
</tbody>
</table>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>GWAS_table</strong> (<em>pandas dataframe</em>) – GWAS data as a dataframe</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>a pandas dataframe with missing value all equal to np.nan</p>
</dd>
</dl>
</dd></dl>
<dl class="function">
<dt id="jass_preprocessing.map_gwas.gwas_internal_link">
<code class="descclassname">jass_preprocessing.map_gwas.</code><code class="descname">gwas_internal_link</code><span class="sig-paren">(</span><em>GWAS_table</em>, <em>GWAS_path</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/map_gwas.html#gwas_internal_link"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#jass_preprocessing.map_gwas.gwas_internal_link" title="Permalink to this definition"></a></dt>
<code class="sig-prename descclassname">jass_preprocessing.map_gwas.</code><code class="sig-name descname">gwas_internal_link</code><span class="sig-paren">(</span><em class="sig-param">GWAS_table</em>, <em class="sig-param">GWAS_path</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/map_gwas.html#gwas_internal_link"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#jass_preprocessing.map_gwas.gwas_internal_link" title="Permalink to this definition"></a></dt>
<dd><p>Walk the GWAS path to find the GWAS tables</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>GWAS_table</strong> (<em>str</em>) – path of the folder to explore</li>
<li><strong>findfile</strong> (<em>str</em>) – name of the file to find</li>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>GWAS_table</strong> (<em>str</em>) – path of the folder to explore</p></li>
<li><p><strong>findfile</strong> (<em>str</em>) – name of the file to find</p></li>
</ul>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">a pandas dataframe with one column for the filename
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>a pandas dataframe with one column for the filename
and one column containing the complete path to the file</p>
</td>
</tr>
</tbody>
</table>
</dd>
</dl>
</dd></dl>
<dl class="function">
<dt id="jass_preprocessing.map_gwas.map_columns_position">
<code class="descclassname">jass_preprocessing.map_gwas.</code><code class="descname">map_columns_position</code><span class="sig-paren">(</span><em>gwas_internal_link</em>, <em>GWAS_labels</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/map_gwas.html#map_columns_position"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#jass_preprocessing.map_gwas.map_columns_position" title="Permalink to this definition"></a></dt>
<code class="sig-prename descclassname">jass_preprocessing.map_gwas.</code><code class="sig-name descname">map_columns_position</code><span class="sig-paren">(</span><em class="sig-param">gwas_internal_link</em>, <em class="sig-param">column_dict</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/map_gwas.html#map_columns_position"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#jass_preprocessing.map_gwas.map_columns_position" title="Permalink to this definition"></a></dt>
<dd><p>Find column position for each specific Gwas</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>gwas_internal_link</strong> (<em>str</em>) – filename of the GWAS data (with path)</li>
<li><strong>GWAS_labels</strong> (<em>str</em>) – filename of the csv information file</li>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>gwas_internal_link</strong> (<em>str</em>) – filename of the GWAS data (with path)</p></li>
<li><p><strong>GWAS_labels</strong> (<em>pd.DataFrame</em>) – corresponding row of the information file</p></li>
</ul>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">pandas Series with column position and column names as index</p>
</td>
</tr>
</tbody>
</table>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>pandas Series with column position and column names as index</p>
</dd>
</dl>
</dd></dl>
<dl class="function">
<dt id="jass_preprocessing.map_gwas.read_gwas">
<code class="descclassname">jass_preprocessing.map_gwas.</code><code class="descname">read_gwas</code><span class="sig-paren">(</span><em>gwas_internal_link</em>, <em>column_map</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/map_gwas.html#read_gwas"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#jass_preprocessing.map_gwas.read_gwas" title="Permalink to this definition"></a></dt>
<code class="sig-prename descclassname">jass_preprocessing.map_gwas.</code><code class="sig-name descname">read_gwas</code><span class="sig-paren">(</span><em class="sig-param">gwas_internal_link</em>, <em class="sig-param">column_map</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/map_gwas.html#read_gwas"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#jass_preprocessing.map_gwas.read_gwas" title="Permalink to this definition"></a></dt>
<dd><p>Read gwas raw data, fetch columns thanks to position stored in
column_map and rename columns according to column_map.index</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>gwas_internal_link</strong> (<em>str</em>) – GWAS data as a dataframe</li>
<li><strong>column_map</strong> (<em>pandas Series</em>) – Series containing the position of column in</li>
<li><strong>raw data</strong> (<em>the</em>) – </li>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>gwas_internal_link</strong> (<em>str</em>) – GWAS data as a dataframe</p></li>
<li><p><strong>column_map</strong> (<em>pandas Series</em>) – Series containing the position of column in</p></li>
<li><p><strong>raw data</strong> (<em>the</em>) – </p></li>
</ul>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">a pandas dataframe with missing value all equal to np.nan</p>
</td>
</tr>
</tbody>
</table>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>a pandas dataframe with missing value all equal to np.nan</p>
</dd>
</dl>
</dd></dl>
<dl class="function">
<dt id="jass_preprocessing.map_gwas.walkfs">
<code class="descclassname">jass_preprocessing.map_gwas.</code><code class="descname">walkfs</code><span class="sig-paren">(</span><em>startdir</em>, <em>findfile</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/map_gwas.html#walkfs"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#jass_preprocessing.map_gwas.walkfs" title="Permalink to this definition"></a></dt>
<code class="sig-prename descclassname">jass_preprocessing.map_gwas.</code><code class="sig-name descname">walkfs</code><span class="sig-paren">(</span><em class="sig-param">startdir</em>, <em class="sig-param">findfile</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/map_gwas.html#walkfs"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#jass_preprocessing.map_gwas.walkfs" title="Permalink to this definition"></a></dt>
<dd><p>Go through the folder and subfolder to find the specified file</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>startdir</strong> (<em>str</em>) – path of the folder to explore</li>
<li><strong>findfile</strong> (<em>str</em>) – name of the file to find</li>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>startdir</strong> (<em>str</em>) – path of the folder to explore</p></li>
<li><p><strong>findfile</strong> (<em>str</em>) – name of the file to find</p></li>
</ul>
</td>
</tr>
</tbody>
</table>
</dd>
</dl>
</dd></dl>
</div>
......@@ -297,7 +281,7 @@ column_map and rename columns according to column_map.index</p>
<p>Module of function</p>
<dl class="function">
<dt id="jass_preprocessing.map_reference.compute_is_aligned">
<code class="descclassname">jass_preprocessing.map_reference.</code><code class="descname">compute_is_aligned</code><span class="sig-paren">(</span><em>mgwas</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/map_reference.html#compute_is_aligned"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#jass_preprocessing.map_reference.compute_is_aligned" title="Permalink to this definition"></a></dt>
<code class="sig-prename descclassname">jass_preprocessing.map_reference.</code><code class="sig-name descname">compute_is_aligned</code><span class="sig-paren">(</span><em class="sig-param">mgwas</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/map_reference.html#compute_is_aligned"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#jass_preprocessing.map_reference.compute_is_aligned" title="Permalink to this definition"></a></dt>
<dd><p>Check if the reference panel and the GWAS data have the same reference
allele. return a boolean vector.
The function should be the complement of “is_flipped” but we still compute
......@@ -307,63 +291,77 @@ instance)</p>
<dl class="function">
<dt id="jass_preprocessing.map_reference.compute_is_flipped">
<code class="descclassname">jass_preprocessing.map_reference.</code><code class="descname">compute_is_flipped</code><span class="sig-paren">(</span><em>mgwas</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/map_reference.html#compute_is_flipped"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#jass_preprocessing.map_reference.compute_is_flipped" title="Permalink to this definition"></a></dt>
<code class="sig-prename descclassname">jass_preprocessing.map_reference.</code><code class="sig-name descname">compute_is_flipped</code><span class="sig-paren">(</span><em class="sig-param">mgwas</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/map_reference.html#compute_is_flipped"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#jass_preprocessing.map_reference.compute_is_flipped" title="Permalink to this definition"></a></dt>
<dd><p>Check if the reference panel and the GWAS data have the same reference
allele. return a boolean vector.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>mgwas</strong> (<em>pandas dataframe</em>) – GWAS study dataframe merged with the reference_panel</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">merge studies,</td>
</tr>
<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body">is_flipped (pandas dataframe)</td>
</tr>
</tbody>
</table>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>mgwas</strong> (<em>pandas dataframe</em>) – GWAS study dataframe merged with the reference_panel</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>merge studies,</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p>is_flipped (pandas dataframe)</p>
</dd>
</dl>
</dd></dl>
<dl class="function">
<dt id="jass_preprocessing.map_reference.compute_snp_alignement">
<code class="descclassname">jass_preprocessing.map_reference.</code><code class="descname">compute_snp_alignement</code><span class="sig-paren">(</span><em>mgwas</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/map_reference.html#compute_snp_alignement"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#jass_preprocessing.map_reference.compute_snp_alignement" title="Permalink to this definition"></a></dt>
<code class="sig-prename descclassname">jass_preprocessing.map_reference.</code><code class="sig-name descname">compute_snp_alignement</code><span class="sig-paren">(</span><em class="sig-param">mgwas</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/map_reference.html#compute_snp_alignement"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#jass_preprocessing.map_reference.compute_snp_alignement" title="Permalink to this definition"></a></dt>
<dd><p>Add a column to mgwas indicating if the reference and coded
allele is flipped compared to the reference panel.
If it is, the sign of the statistic must be flipped
:param mgwas: a pandas dataframe of the GWAS data merged</p>
<blockquote>
<div>with the reference panel</div></blockquote>
<div><p>with the reference panel</p>
</div></blockquote>
</dd></dl>
<dl class="function">
<dt id="jass_preprocessing.map_reference.map_on_ref_panel">
<code class="descclassname">jass_preprocessing.map_reference.</code><code class="descname">map_on_ref_panel</code><span class="sig-paren">(</span><em>gw_df</em>, <em>ref_panel</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/map_reference.html#map_on_ref_panel"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#jass_preprocessing.map_reference.map_on_ref_panel" title="Permalink to this definition"></a></dt>
<code class="sig-prename descclassname">jass_preprocessing.map_reference.</code><code class="sig-name descname">map_on_ref_panel</code><span class="sig-paren">(</span><em class="sig-param">gw_df</em>, <em class="sig-param">ref_panel</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/map_reference.html#map_on_ref_panel"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#jass_preprocessing.map_reference.map_on_ref_panel" title="Permalink to this definition"></a></dt>
<dd><p>Merge Gwas dataframe with the reference panel
Make sure that the same SNPs are in the reference panel and the gwas</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>gw_df</strong> (<em>pandas dataframe</em>) – GWAS study dataframe</li>
<li><strong>ref_panel</strong> (<em>pandas dataframe</em>) – reference panel dataframe</li>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>gw_df</strong> (<em>pandas dataframe</em>) – GWAS study dataframe</p></li>
<li><p><strong>ref_panel</strong> (<em>pandas dataframe</em>) – reference panel dataframe</p></li>
</ul>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">merge studies,</p>
</td>
</tr>
<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last">merge_GWAS (pandas dataframe)</p>
</td>
</tr>
</tbody>
</table>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>merge studies,</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p>merge_GWAS (pandas dataframe)</p>
</dd>
</dl>
</dd></dl>
<dl class="function">
<dt id="jass_preprocessing.map_reference.read_reference">
<code class="descclassname">jass_preprocessing.map_reference.</code><code class="descname">read_reference</code><span class="sig-paren">(</span><em>gwas_reference_panel</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/map_reference.html#read_reference"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#jass_preprocessing.map_reference.read_reference" title="Permalink to this definition"></a></dt>
<dd><p>helper function to name correctly the column</p>
<code class="sig-prename descclassname">jass_preprocessing.map_reference.</code><code class="sig-name descname">read_reference</code><span class="sig-paren">(</span><em class="sig-param">gwas_reference_panel</em>, <em class="sig-param">mask_MHC=False</em>, <em class="sig-param">minimum_MAF=None</em>, <em class="sig-param">region_to_mask=None</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/map_reference.html#read_reference"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#jass_preprocessing.map_reference.read_reference" title="Permalink to this definition"></a></dt>
<dd><p>helper function to name correctly the column
:param gwas_reference_panel: path toward the reference panel file
:type gwas_reference_panel: str
:param mask_MHC: Whether the MHC region should be masked or not. default is False
:type mask_MHC: bool
:param Filter the reference panel by minimum allele frequency:
:type Filter the reference panel by minimum allele frequency: hg19 coordinate
:param minimum_MAF: minimum allele frequency for a SNPs to be retain in the panel
:type minimum_MAF: float
:param region_to_mask: a list of additional regions to mask
:type region_to_mask: dict</p>
<dl class="field-list simple">
<dt class="field-odd">Returns</dt>
<dd class="field-odd"><p>the reference_panel with the specified filter applied</p>
</dd>
<dt class="field-even">Return type</dt>
<dd class="field-even"><p>ref (pandas dataframe)</p>
</dd>
</dl>
</dd></dl>
</div>
......@@ -371,39 +369,39 @@ Make sure that the same SNPs are in the reference panel and the gwas</p>
<span id="jass-preprocessing-save-output-module"></span><h2>jass_preprocessing.save_output module<a class="headerlink" href="#module-jass_preprocessing.save_output" title="Permalink to this headline"></a></h2>
<dl class="function">
<dt id="jass_preprocessing.save_output.save_output">
<code class="descclassname">jass_preprocessing.save_output.</code><code class="descname">save_output</code><span class="sig-paren">(</span><em>mgwas</em>, <em>ImpG_output_Folder</em>, <em>my_study</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/save_output.html#save_output"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#jass_preprocessing.save_output.save_output" title="Permalink to this definition"></a></dt>
<code class="sig-prename descclassname">jass_preprocessing.save_output.</code><code class="sig-name descname">save_output</code><span class="sig-paren">(</span><em class="sig-param">mgwas</em>, <em class="sig-param">ImpG_output_Folder</em>, <em class="sig-param">my_study</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/save_output.html#save_output"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#jass_preprocessing.save_output.save_output" title="Permalink to this definition"></a></dt>
<dd><p>Write the preprocessed Gwas for ldscore analysis</p>
</dd></dl>
<dl class="function">
<dt id="jass_preprocessing.save_output.save_output_by_chromosome">
<code class="descclassname">jass_preprocessing.save_output.</code><code class="descname">save_output_by_chromosome</code><span class="sig-paren">(</span><em>mgwas</em>, <em>ImpG_output_Folder</em>, <em>my_study</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/save_output.html#save_output_by_chromosome"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#jass_preprocessing.save_output.save_output_by_chromosome" title="Permalink to this definition"></a></dt>
<code class="sig-prename descclassname">jass_preprocessing.save_output.</code><code class="sig-name descname">save_output_by_chromosome</code><span class="sig-paren">(</span><em class="sig-param">mgwas</em>, <em class="sig-param">ImpG_output_Folder</em>, <em class="sig-param">my_study</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/save_output.html#save_output_by_chromosome"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#jass_preprocessing.save_output.save_output_by_chromosome" title="Permalink to this definition"></a></dt>
<dd><p>Write the preprocessed Gwas for imputation</p>
</dd></dl>
</div>
<div class="section" id="module-jass_preprocessing">
<span id="module-contents"></span><h2>Module contents<a class="headerlink" href="#module-jass_preprocessing" title="Permalink to this headline"></a></h2>
<table border="1" class="longtable docutils">
<table class="longtable docutils align-default">
<colgroup>
<col width="10%" />
<col width="90%" />
<col style="width: 10%" />
<col style="width: 90%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="#module-jass_preprocessing.map_gwas" title="jass_preprocessing.map_gwas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">map_gwas</span></code></a></td>
<td>Map GWAS</td>
<tbody>
<tr class="row-odd"><td><p><a class="reference internal" href="#module-jass_preprocessing.map_gwas" title="jass_preprocessing.map_gwas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">map_gwas</span></code></a></p></td>
<td><p>Map GWAS</p></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#module-jass_preprocessing.dna_utils" title="jass_preprocessing.dna_utils"><code class="xref py py-obj docutils literal notranslate"><span class="pre">dna_utils</span></code></a></td>
<td>Few fonction to to compute DNA complement</td>
<tr class="row-even"><td><p><a class="reference internal" href="#module-jass_preprocessing.dna_utils" title="jass_preprocessing.dna_utils"><code class="xref py py-obj docutils literal notranslate"><span class="pre">dna_utils</span></code></a></p></td>
<td><p>Few fonction to to compute DNA complement</p></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#module-jass_preprocessing.map_reference" title="jass_preprocessing.map_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">map_reference</span></code></a></td>
<td>Module of function</td>
<tr class="row-odd"><td><p><a class="reference internal" href="#module-jass_preprocessing.map_reference" title="jass_preprocessing.map_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">map_reference</span></code></a></p></td>
<td><p>Module of function</p></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#module-jass_preprocessing.compute_score" title="jass_preprocessing.compute_score"><code class="xref py py-obj docutils literal notranslate"><span class="pre">compute_score</span></code></a></td>
<td></td>
<tr class="row-even"><td><p><a class="reference internal" href="#module-jass_preprocessing.compute_score" title="jass_preprocessing.compute_score"><code class="xref py py-obj docutils literal notranslate"><span class="pre">compute_score</span></code></a></p></td>
<td><p></p></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#module-jass_preprocessing.save_output" title="jass_preprocessing.save_output"><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_output</span></code></a></td>
<td></td>
<tr class="row-odd"><td><p><a class="reference internal" href="#module-jass_preprocessing.save_output" title="jass_preprocessing.save_output"><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_output</span></code></a></p></td>
<td><p></p></td>
</tr>
</tbody>
</table>
......@@ -438,25 +436,16 @@ Make sure that the same SNPs are in the reference panel and the gwas</p>
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......@@ -154,9 +156,7 @@
<li class="toctree-l2"><a class="reference internal" href="jass_preprocessing.html#module-jass_preprocessing.map_gwas">jass_preprocessing.map_gwas module</a></li>
<li class="toctree-l2"><a class="reference internal" href="jass_preprocessing.html#module-jass_preprocessing.map_reference">jass_preprocessing.map_reference module</a></li>
<li class="toctree-l2"><a class="reference internal" href="jass_preprocessing.html#module-jass_preprocessing.save_output">jass_preprocessing.save_output module</a></li>
<li class="toctree-l2"><a class="reference internal" href="jass_preprocessing.html#module-jass_preprocessing">Module contents</a><ul class="simple">
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<li class="toctree-l2"><a class="reference internal" href="jass_preprocessing.html#module-jass_preprocessing">Module contents</a></li>
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......@@ -191,25 +191,16 @@
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