diff --git a/doc/_build/doctrees/_autosummary/jass_preprocessing.doctree b/doc/_build/doctrees/_autosummary/jass_preprocessing.doctree
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Binary files a/doc/_build/doctrees/_autosummary/jass_preprocessing.doctree and b/doc/_build/doctrees/_autosummary/jass_preprocessing.doctree differ
diff --git a/doc/_build/doctrees/_autosummary/modules.doctree b/doc/_build/doctrees/_autosummary/modules.doctree
index 27e69465a3f3a5f52f0a552a07a3b5fae79b0de3..adbb1224878275e58a1f99845253ac74761f99f4 100644
Binary files a/doc/_build/doctrees/_autosummary/modules.doctree and b/doc/_build/doctrees/_autosummary/modules.doctree differ
diff --git a/doc/_build/doctrees/environment.pickle b/doc/_build/doctrees/environment.pickle
index f5c71c806c0033c18802de52f9650f07ccba2a70..0e2a4461c68e576828433c99f3dd95c1b29d96f5 100644
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diff --git a/doc/_build/doctrees/index.doctree b/doc/_build/doctrees/index.doctree
index 6e782da42779c8fdf7cc36eff0048a4115c4ebed..3a79313c70a1d3ffaa95b8b69159c0c2db221dcd 100644
Binary files a/doc/_build/doctrees/index.doctree and b/doc/_build/doctrees/index.doctree differ
diff --git a/doc/_build/html/.buildinfo b/doc/_build/html/.buildinfo
index d4001700a5cc33291156a913bc4f82fc1f733f82..b684fa9e556bf21dbbc0ed48453a805f5612bf48 100644
--- a/doc/_build/html/.buildinfo
+++ b/doc/_build/html/.buildinfo
@@ -1,4 +1,4 @@
# Sphinx build info version 1
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 7890896c7cf0d3614ade393a5c103246
+config: f0cd103aab646a141229409df671f02e
tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/doc/_build/html/_autosummary/jass_preprocessing.html b/doc/_build/html/_autosummary/jass_preprocessing.html
index 573ab6b3f170548f62ad9a8f93e5098280342494..3cbc00302996a914b4b78800e989afbad3870ea7 100644
--- a/doc/_build/html/_autosummary/jass_preprocessing.html
+++ b/doc/_build/html/_autosummary/jass_preprocessing.html
@@ -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>
+ <script type="text/javascript" src="../_static/jquery.js"></script>
+ <script type="text/javascript" src="../_static/underscore.js"></script>
+ <script type="text/javascript" src="../_static/doctools.js"></script>
+ <script type="text/javascript" src="../_static/language_data.js"></script>
+
+ <script type="text/javascript" src="../_static/js/theme.js"></script>
-
+
+
<link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
-
-
- <script src="../_static/js/modernizr.min.js"></script>
-
</head>
<body class="wy-body-for-nav">
<div class="wy-grid-for-nav">
-
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
<div class="wy-side-scroll">
- <div class="wy-side-nav-search">
+ <div class="wy-side-nav-search" >
@@ -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>
-
-
-
-
- <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
- <script type="text/javascript" src="../_static/jquery.js"></script>
- <script type="text/javascript" src="../_static/underscore.js"></script>
- <script type="text/javascript" src="../_static/doctools.js"></script>
-
-
-
-
- <script type="text/javascript" src="../_static/js/theme.js"></script>
-
<script type="text/javascript">
jQuery(function () {
SphinxRtdTheme.Navigation.enable(true);
});
- </script>
+ </script>
+
+
+
+
+
</body>
</html>
\ No newline at end of file
diff --git a/doc/_build/html/_autosummary/modules.html b/doc/_build/html/_autosummary/modules.html
index 889969b83af8690f63dda023cdc3bbc2880dcfa8..1e41c94b01d52fe1c16250ec423862746f327580 100644
--- a/doc/_build/html/_autosummary/modules.html
+++ b/doc/_build/html/_autosummary/modules.html
@@ -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>
+ <script type="text/javascript" src="../_static/jquery.js"></script>
+ <script type="text/javascript" src="../_static/underscore.js"></script>
+ <script type="text/javascript" src="../_static/doctools.js"></script>
+ <script type="text/javascript" src="../_static/language_data.js"></script>
+
+ <script type="text/javascript" src="../_static/js/theme.js"></script>
-
+
+
<link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
-
-
- <script src="../_static/js/modernizr.min.js"></script>
-
</head>
<body class="wy-body-for-nav">
<div class="wy-grid-for-nav">
-
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
<div class="wy-side-scroll">
- <div class="wy-side-nav-search">
+ <div class="wy-side-nav-search" >
@@ -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">
-</ul>
-</li>
+<li class="toctree-l2"><a class="reference internal" href="jass_preprocessing.html#module-jass_preprocessing">Module contents</a></li>
</ul>
</li>
</ul>
@@ -191,25 +191,16 @@
-
-
-
-
- <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
- <script type="text/javascript" src="../_static/jquery.js"></script>
- <script type="text/javascript" src="../_static/underscore.js"></script>
- <script type="text/javascript" src="../_static/doctools.js"></script>
-
-
-
-
- <script type="text/javascript" src="../_static/js/theme.js"></script>
-
<script type="text/javascript">
jQuery(function () {
SphinxRtdTheme.Navigation.enable(true);
});
- </script>
+ </script>
+
+
+
+
+
</body>
</html>
\ No newline at end of file
diff --git a/doc/_build/html/_modules/index.html b/doc/_build/html/_modules/index.html
index e6e25eec70198b637d0b16d1d4adb236902341d7..685e6106699aabffd33ffbec37fabb32553d5095 100644
--- a/doc/_build/html/_modules/index.html
+++ b/doc/_build/html/_modules/index.html
@@ -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>
+ <script type="text/javascript" src="../_static/jquery.js"></script>
+ <script type="text/javascript" src="../_static/underscore.js"></script>
+ <script type="text/javascript" src="../_static/doctools.js"></script>
+ <script type="text/javascript" src="../_static/language_data.js"></script>
+
+ <script type="text/javascript" src="../_static/js/theme.js"></script>
-
+
+
<link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
-
-
- <script src="../_static/js/modernizr.min.js"></script>
-
</head>
<body class="wy-body-for-nav">
<div class="wy-grid-for-nav">
-
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
<div class="wy-side-scroll">
- <div class="wy-side-nav-search">
+ <div class="wy-side-nav-search" >
@@ -171,25 +173,16 @@
-
-
-
-
- <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
- <script type="text/javascript" src="../_static/jquery.js"></script>
- <script type="text/javascript" src="../_static/underscore.js"></script>
- <script type="text/javascript" src="../_static/doctools.js"></script>
-
-
-
-
- <script type="text/javascript" src="../_static/js/theme.js"></script>
-
<script type="text/javascript">
jQuery(function () {
SphinxRtdTheme.Navigation.enable(true);
});
- </script>
+ </script>
+
+
+
+
+
</body>
</html>
\ No newline at end of file
diff --git a/doc/_build/html/_modules/jass_preprocessing/compute_score.html b/doc/_build/html/_modules/jass_preprocessing/compute_score.html
index 98653d3f499163f7bb332b1efe50b191951cc632..5f539047195caef3eea3cdaa79c4daf6ef95fd2c 100644
--- a/doc/_build/html/_modules/jass_preprocessing/compute_score.html
+++ b/doc/_build/html/_modules/jass_preprocessing/compute_score.html
@@ -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>
+ <script type="text/javascript" src="../../_static/jquery.js"></script>
+ <script type="text/javascript" src="../../_static/underscore.js"></script>
+ <script type="text/javascript" src="../../_static/doctools.js"></script>
+ <script type="text/javascript" src="../../_static/language_data.js"></script>
+
+ <script type="text/javascript" src="../../_static/js/theme.js"></script>
-
+
+
<link rel="stylesheet" href="../../_static/css/theme.css" type="text/css" />
<link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
<link rel="index" title="Index" href="../../genindex.html" />
<link rel="search" title="Search" href="../../search.html" />
-
-
- <script src="../../_static/js/modernizr.min.js"></script>
-
</head>
<body class="wy-body-for-nav">
<div class="wy-grid-for-nav">
-
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
<div class="wy-side-scroll">
- <div class="wy-side-nav-search">
+ <div class="wy-side-nav-search" >
@@ -147,7 +149,7 @@
<span class="kn">import</span> <span class="nn">seaborn</span> <span class="k">as</span> <span class="nn">sns</span>
<span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="k">as</span> <span class="nn">plt</span>
-<span class="n">perSS</span> <span class="o">=</span> <span class="mf">0.7</span>
+
<div class="viewcode-block" id="compute_z_score"><a class="viewcode-back" href="../../_autosummary/jass_preprocessing.html#jass_preprocessing.compute_score.compute_z_score">[docs]</a><span class="k">def</span> <span class="nf">compute_z_score</span><span class="p">(</span><span class="n">mgwas</span><span class="p">):</span>
<span class="sd">"""</span>
@@ -168,7 +170,7 @@
<span class="k">return</span> <span class="n">mgwas</span></div>
-<div class="viewcode-block" id="compute_sample_size"><a class="viewcode-back" href="../../_autosummary/jass_preprocessing.html#jass_preprocessing.compute_score.compute_sample_size">[docs]</a><span class="k">def</span> <span class="nf">compute_sample_size</span><span class="p">(</span><span class="n">mgwas</span><span class="p">,</span> <span class="n">diagnostic_folder</span><span class="p">,</span> <span class="n">trait</span><span class="p">):</span>
+<div class="viewcode-block" id="compute_sample_size"><a class="viewcode-back" href="../../_autosummary/jass_preprocessing.html#jass_preprocessing.compute_score.compute_sample_size">[docs]</a><span class="k">def</span> <span class="nf">compute_sample_size</span><span class="p">(</span><span class="n">mgwas</span><span class="p">,</span> <span class="n">diagnostic_folder</span><span class="p">,</span> <span class="n">trait</span><span class="p">,</span> <span class="n">perSS</span> <span class="o">=</span> <span class="mf">0.7</span><span class="p">):</span>
<span class="k">if</span> <span class="s1">'n'</span> <span class="ow">in</span> <span class="n">mgwas</span><span class="o">.</span><span class="n">columns</span><span class="p">:</span>
<span class="n">myN</span> <span class="o">=</span> <span class="n">mgwas</span><span class="o">.</span><span class="n">n</span>
@@ -192,7 +194,7 @@
<span class="n">warnings</span><span class="o">.</span><span class="n">warn</span><span class="p">(</span><span class="s2">"Some snp had an infinite sample size"</span><span class="p">)</span>
<span class="n">myW_thres</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">percentile</span><span class="p">(</span><span class="n">myN</span><span class="o">.</span><span class="n">dropna</span><span class="p">(),</span> <span class="mi">90</span><span class="p">)</span>
- <span class="n">ss_thres</span> <span class="o">=</span> <span class="n">perSS</span> <span class="o">*</span> <span class="n">myW_thres</span>
+ <span class="n">ss_thres</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">perSS</span><span class="p">)</span> <span class="o">*</span> <span class="n">myW_thres</span>
<span class="n">mgwas</span><span class="p">[</span><span class="s2">"computed_N"</span><span class="p">]</span> <span class="o">=</span> <span class="n">myN</span>
<span class="n">plt</span><span class="o">.</span><span class="n">clf</span><span class="p">()</span>
<span class="n">p1</span> <span class="o">=</span> <span class="n">sns</span><span class="o">.</span><span class="n">distplot</span><span class="p">(</span><span class="n">mgwas</span><span class="o">.</span><span class="n">computed_N</span><span class="p">[</span><span class="o">~</span><span class="n">mgwas</span><span class="o">.</span><span class="n">computed_N</span><span class="o">.</span><span class="n">isna</span><span class="p">()])</span>
@@ -235,25 +237,16 @@
-
-
-
-
- <script type="text/javascript" id="documentation_options" data-url_root="../../" src="../../_static/documentation_options.js"></script>
- <script type="text/javascript" src="../../_static/jquery.js"></script>
- <script type="text/javascript" src="../../_static/underscore.js"></script>
- <script type="text/javascript" src="../../_static/doctools.js"></script>
-
-
-
-
- <script type="text/javascript" src="../../_static/js/theme.js"></script>
-
<script type="text/javascript">
jQuery(function () {
SphinxRtdTheme.Navigation.enable(true);
});
- </script>
+ </script>
+
+
+
+
+
</body>
</html>
\ No newline at end of file
diff --git a/doc/_build/html/_modules/jass_preprocessing/dna_utils.html b/doc/_build/html/_modules/jass_preprocessing/dna_utils.html
index c30ed3bd95e16da043b8cb7995d4e9210312c35c..431e99d46d749bee608385325ce385c62ae18b2e 100644
--- a/doc/_build/html/_modules/jass_preprocessing/dna_utils.html
+++ b/doc/_build/html/_modules/jass_preprocessing/dna_utils.html
@@ -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>
+ <script type="text/javascript" src="../../_static/jquery.js"></script>
+ <script type="text/javascript" src="../../_static/underscore.js"></script>
+ <script type="text/javascript" src="../../_static/doctools.js"></script>
+ <script type="text/javascript" src="../../_static/language_data.js"></script>
+
+ <script type="text/javascript" src="../../_static/js/theme.js"></script>
-
+
+
<link rel="stylesheet" href="../../_static/css/theme.css" type="text/css" />
<link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
<link rel="index" title="Index" href="../../genindex.html" />
<link rel="search" title="Search" href="../../search.html" />
-
-
- <script src="../../_static/js/modernizr.min.js"></script>
-
</head>
<body class="wy-body-for-nav">
<div class="wy-grid-for-nav">
-
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
<div class="wy-side-scroll">
- <div class="wy-side-nav-search">
+ <div class="wy-side-nav-search" >
@@ -183,25 +185,16 @@
-
-
-
-
- <script type="text/javascript" id="documentation_options" data-url_root="../../" src="../../_static/documentation_options.js"></script>
- <script type="text/javascript" src="../../_static/jquery.js"></script>
- <script type="text/javascript" src="../../_static/underscore.js"></script>
- <script type="text/javascript" src="../../_static/doctools.js"></script>
-
-
-
-
- <script type="text/javascript" src="../../_static/js/theme.js"></script>
-
<script type="text/javascript">
jQuery(function () {
SphinxRtdTheme.Navigation.enable(true);
});
- </script>
+ </script>
+
+
+
+
+
</body>
</html>
\ No newline at end of file
diff --git a/doc/_build/html/_modules/jass_preprocessing/map_gwas.html b/doc/_build/html/_modules/jass_preprocessing/map_gwas.html
index ec7b4140ecbad83c62ed14a47c3a91bc98dd442b..0cbd1a37a6dc7374ba5b02b22212c807640724d0 100644
--- a/doc/_build/html/_modules/jass_preprocessing/map_gwas.html
+++ b/doc/_build/html/_modules/jass_preprocessing/map_gwas.html
@@ -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>
+ <script type="text/javascript" src="../../_static/jquery.js"></script>
+ <script type="text/javascript" src="../../_static/underscore.js"></script>
+ <script type="text/javascript" src="../../_static/doctools.js"></script>
+ <script type="text/javascript" src="../../_static/language_data.js"></script>
+
+ <script type="text/javascript" src="../../_static/js/theme.js"></script>
-
+
+
<link rel="stylesheet" href="../../_static/css/theme.css" type="text/css" />
<link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
<link rel="index" title="Index" href="../../genindex.html" />
<link rel="search" title="Search" href="../../search.html" />
-
-
- <script src="../../_static/js/modernizr.min.js"></script>
-
</head>
<body class="wy-body-for-nav">
<div class="wy-grid-for-nav">
-
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
<div class="wy-side-scroll">
- <div class="wy-side-nav-search">
+ <div class="wy-side-nav-search" >
@@ -151,6 +153,9 @@
<span class="kn">import</span> <span class="nn">sys</span>
<span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
+<span class="kn">import</span> <span class="nn">gzip</span>
+<span class="kn">import</span> <span class="nn">re</span>
+
<div class="viewcode-block" id="walkfs"><a class="viewcode-back" href="../../_autosummary/jass_preprocessing.html#jass_preprocessing.map_gwas.walkfs">[docs]</a><span class="k">def</span> <span class="nf">walkfs</span><span class="p">(</span><span class="n">startdir</span><span class="p">,</span> <span class="n">findfile</span><span class="p">):</span>
<span class="sd">"""</span>
@@ -214,46 +219,48 @@
<span class="k">return</span> <span class="n">df</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="n">def_missing</span><span class="p">,</span> <span class="n">nan_vec</span><span class="p">)</span></div>
-<div class="viewcode-block" id="map_columns_position"><a class="viewcode-back" href="../../_autosummary/jass_preprocessing.html#jass_preprocessing.map_gwas.map_columns_position">[docs]</a><span class="k">def</span> <span class="nf">map_columns_position</span><span class="p">(</span><span class="n">gwas_internal_link</span><span class="p">,</span> <span class="n">GWAS_labels</span><span class="p">):</span>
+<div class="viewcode-block" id="map_columns_position"><a class="viewcode-back" href="../../_autosummary/jass_preprocessing.html#jass_preprocessing.map_gwas.map_columns_position">[docs]</a><span class="k">def</span> <span class="nf">map_columns_position</span><span class="p">(</span><span class="n">gwas_internal_link</span><span class="p">,</span> <span class="n">column_dict</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Find column position for each specific Gwas</span>
<span class="sd"> Args:</span>
<span class="sd"> gwas_internal_link (str): filename of the GWAS data (with path)</span>
-<span class="sd"> GWAS_labels (str): filename of the csv information file</span>
+<span class="sd"> GWAS_labels (pd.DataFrame): corresponding row of the information file</span>
<span class="sd"> Return:</span>
<span class="sd"> pandas Series with column position and column names as index</span>
<span class="sd"> """</span>
- <span class="n">column_dict</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="n">GWAS_labels</span><span class="p">,</span> <span class="n">sep</span><span class="o">=</span><span class="s1">'</span><span class="se">\t</span><span class="s1">'</span><span class="p">,</span> <span class="n">na_values</span><span class="o">=</span><span class="s1">'na'</span><span class="p">,</span> <span class="n">index_col</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
-
+ <span class="nb">print</span><span class="p">(</span><span class="n">gwas_internal_link</span><span class="p">)</span>
<span class="n">gwas_file</span> <span class="o">=</span> <span class="n">gwas_internal_link</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">'/'</span><span class="p">)[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
-
- <span class="n">my_labels</span> <span class="o">=</span> <span class="n">column_dict</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">gwas_file</span><span class="p">]</span>
-
<span class="c1">#Our standart labels:</span>
- <span class="n">reference_label</span> <span class="o">=</span> <span class="n">column_dict</span><span class="o">.</span><span class="n">columns</span><span class="o">.</span><span class="n">tolist</span><span class="p">()</span>
- <span class="c1"># labels in the GWAS files</span>
- <span class="n">target_lab</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">Index</span><span class="p">(</span><span class="n">my_labels</span><span class="o">.</span><span class="n">values</span><span class="o">.</span><span class="n">tolist</span><span class="p">())</span>
- <span class="n">f</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">gwas_internal_link</span><span class="p">)</span>
+ <span class="n">reference_label</span> <span class="o">=</span> <span class="n">column_dict</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">tolist</span><span class="p">()</span>
+ <span class="nb">print</span><span class="p">(</span><span class="n">reference_label</span><span class="p">)</span>
+ <span class="c1"># labels in the GWAS files</span>
+ <span class="n">target_lab</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">Index</span><span class="p">(</span><span class="n">column_dict</span><span class="o">.</span><span class="n">values</span><span class="o">.</span><span class="n">tolist</span><span class="p">())</span>
+ <span class="n">is_gzipped</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="sa">r</span><span class="s2">".gz$"</span><span class="p">,</span> <span class="n">gwas_internal_link</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">is_gzipped</span><span class="p">:</span>
+ <span class="n">f</span> <span class="o">=</span> <span class="n">gzip</span><span class="o">.</span><span class="n">open</span><span class="p">(</span><span class="n">gwas_internal_link</span><span class="p">)</span>
+ <span class="n">line</span> <span class="o">=</span> <span class="n">f</span><span class="o">.</span><span class="n">readline</span><span class="p">()</span>
+ <span class="n">line</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">decode</span><span class="p">(</span><span class="s1">'utf-8'</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">f</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">gwas_internal_link</span><span class="p">)</span>
+ <span class="n">line</span> <span class="o">=</span> <span class="n">f</span><span class="o">.</span><span class="n">readline</span><span class="p">()</span>
<span class="n">count_line</span> <span class="o">=</span> <span class="mi">0</span>
- <span class="n">line</span> <span class="o">=</span> <span class="n">f</span><span class="o">.</span><span class="n">readline</span><span class="p">()</span>
- <span class="nb">print</span><span class="p">(</span><span class="n">line</span><span class="p">)</span>
- <span class="n">header</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">Index</span><span class="p">(</span><span class="n">line</span><span class="o">.</span><span class="n">split</span><span class="p">())</span>
+ <span class="n">header</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">Index</span><span class="p">(</span><span class="n">line</span><span class="o">.</span><span class="n">split</span><span class="p">())</span>
<span class="k">def</span> <span class="nf">get_position</span><span class="p">(</span><span class="n">I</span><span class="p">,</span><span class="n">x</span><span class="p">):</span>
<span class="k">try</span><span class="p">:</span>
<span class="k">return</span> <span class="n">I</span><span class="o">.</span><span class="n">get_loc</span><span class="p">(</span><span class="n">x</span><span class="p">)</span>
<span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span>
<span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">nan</span>
- <span class="n">label_position</span> <span class="o">=</span> <span class="p">[</span><span class="n">get_position</span><span class="p">(</span><span class="n">header</span><span class="p">,</span><span class="n">i</span><span class="p">)</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">target_lab</span><span class="p">]</span>
+ <span class="n">label_position</span> <span class="o">=</span> <span class="p">[</span><span class="n">get_position</span><span class="p">(</span><span class="n">header</span><span class="p">,</span><span class="n">i</span><span class="p">)</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">target_lab</span><span class="p">]</span>
<span class="n">mapgw</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">Series</span><span class="p">(</span><span class="n">label_position</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="n">reference_label</span><span class="p">)</span>
<span class="n">mapgw</span> <span class="o">=</span> <span class="n">mapgw</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="o">~</span><span class="n">mapgw</span><span class="o">.</span><span class="n">isna</span><span class="p">()]</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="nb">int</span><span class="p">)</span>
<span class="n">mapgw</span><span class="o">.</span><span class="n">sort_values</span><span class="p">(</span><span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
- <span class="nb">print</span><span class="p">(</span><span class="n">mapgw</span><span class="p">)</span>
+
<span class="n">f</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
<span class="k">return</span> <span class="n">mapgw</span></div>
@@ -269,18 +276,28 @@
<span class="sd"> Return:</span>
<span class="sd"> a pandas dataframe with missing value all equal to np.nan</span>
<span class="sd"> """</span>
-
+ <span class="nb">print</span><span class="p">(</span><span class="s2">"Reading file:"</span><span class="p">)</span>
+ <span class="nb">print</span><span class="p">(</span><span class="n">gwas_internal_link</span><span class="p">)</span>
+ <span class="n">is_gzipped</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="sa">r</span><span class="s2">".gz$"</span><span class="p">,</span> <span class="n">gwas_internal_link</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">is_gzipped</span><span class="p">:</span>
+ <span class="n">compression</span> <span class="o">=</span> <span class="s1">'gzip'</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">compression</span> <span class="o">=</span> <span class="kc">None</span>
+
+ <span class="nb">print</span><span class="p">(</span><span class="n">column_map</span><span class="o">.</span><span class="n">values</span><span class="p">)</span>
+ <span class="nb">print</span><span class="p">(</span><span class="n">column_map</span><span class="o">.</span><span class="n">index</span><span class="p">)</span>
<span class="n">fullGWAS</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="n">gwas_internal_link</span><span class="p">,</span> <span class="n">delim_whitespace</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
- <span class="n">usecols</span> <span class="o">=</span> <span class="n">column_map</span><span class="o">.</span><span class="n">values</span><span class="p">,</span> <span class="c1">#column_dict['label_position'].keys(),</span>
+ <span class="n">usecols</span> <span class="o">=</span> <span class="n">column_map</span><span class="o">.</span><span class="n">values</span><span class="p">,</span>
+ <span class="n">compression</span><span class="o">=</span><span class="n">compression</span><span class="p">,</span>
+ <span class="c1">#column_dict['label_position'].keys(),</span>
<span class="n">names</span><span class="o">=</span> <span class="n">column_map</span><span class="o">.</span><span class="n">index</span><span class="p">,</span>
- <span class="n">index_col</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span>
- <span class="n">header</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">na_values</span><span class="o">=</span> <span class="p">[</span><span class="s1">''</span><span class="p">,</span> <span class="s1">'#N/A'</span><span class="p">,</span> <span class="s1">'#N/A'</span><span class="p">,</span> <span class="s1">'N/A'</span><span class="p">,</span>
- <span class="s1">'#NA'</span><span class="p">,</span> <span class="s1">'-1.#IND'</span><span class="p">,</span> <span class="s1">'-1.#QNAN'</span><span class="p">,</span>
- <span class="s1">'-NaN'</span><span class="p">,</span>
- <span class="s1">'-nan'</span><span class="p">,</span> <span class="s1">'1.#IND'</span><span class="p">,</span> <span class="s1">'1.#QNAN'</span><span class="p">,</span> <span class="s1">'N/A'</span><span class="p">,</span>
+ <span class="n">header</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">na_values</span><span class="o">=</span> <span class="p">[</span><span class="s1">''</span><span class="p">,</span> <span class="s1">'#N/A'</span><span class="p">,</span> <span class="s1">'#N/A'</span><span class="p">,</span> <span class="s1">'N/A'</span><span class="p">,</span><span class="s1">'#NA'</span><span class="p">,</span> <span class="s1">'-1.#IND'</span><span class="p">,</span> <span class="s1">'-1.#QNAN'</span><span class="p">,</span>
+ <span class="s1">'-NaN'</span><span class="p">,</span> <span class="s1">'-nan'</span><span class="p">,</span> <span class="s1">'1.#IND'</span><span class="p">,</span> <span class="s1">'1.#QNAN'</span><span class="p">,</span> <span class="s1">'N/A'</span><span class="p">,</span>
<span class="s1">'NA'</span><span class="p">,</span> <span class="s1">'NULL'</span><span class="p">,</span> <span class="s1">'NaN'</span><span class="p">,</span>
- <span class="s1">'nan'</span><span class="p">,</span> <span class="s1">'na'</span><span class="p">,</span> <span class="s1">'.'</span><span class="p">])</span>
-
+ <span class="s1">'nan'</span><span class="p">,</span> <span class="s1">'na'</span><span class="p">,</span> <span class="s1">'.'</span><span class="p">,</span> <span class="s1">'-'</span><span class="p">],</span> <span class="n">dtype</span><span class="o">=</span><span class="p">{</span><span class="s2">"snpid"</span><span class="p">:</span><span class="nb">str</span><span class="p">,</span> <span class="s2">"a1"</span><span class="p">:</span><span class="nb">str</span><span class="p">,</span><span class="s2">"a2"</span><span class="p">:</span><span class="nb">str</span><span class="p">,</span><span class="s2">"freq"</span><span class="p">:</span><span class="nb">float</span><span class="p">,</span> <span class="s2">"z"</span><span class="p">:</span><span class="nb">float</span><span class="p">,</span><span class="s2">"se"</span><span class="p">:</span><span class="nb">float</span><span class="p">,</span> <span class="s2">"pval"</span><span class="p">:</span><span class="nb">float</span><span class="p">})</span>
+ <span class="nb">print</span><span class="p">(</span><span class="n">fullGWAS</span><span class="o">.</span><span class="n">head</span><span class="p">())</span>
+ <span class="n">fullGWAS</span><span class="o">.</span><span class="n">set_index</span><span class="p">(</span><span class="s2">"snpid"</span><span class="p">,</span> <span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+ <span class="nb">print</span><span class="p">(</span><span class="n">fullGWAS</span><span class="o">.</span><span class="n">head</span><span class="p">())</span>
<span class="n">fullGWAS</span> <span class="o">=</span> <span class="n">fullGWAS</span><span class="p">[</span><span class="o">~</span><span class="n">fullGWAS</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">duplicated</span><span class="p">(</span><span class="n">keep</span><span class="o">=</span><span class="s1">'first'</span><span class="p">)]</span>
<span class="c1">#fullGWAS = convert_missing_values(fullGWAS)</span>
@@ -314,25 +331,16 @@
-
-
-
-
- <script type="text/javascript" id="documentation_options" data-url_root="../../" src="../../_static/documentation_options.js"></script>
- <script type="text/javascript" src="../../_static/jquery.js"></script>
- <script type="text/javascript" src="../../_static/underscore.js"></script>
- <script type="text/javascript" src="../../_static/doctools.js"></script>
-
-
-
-
- <script type="text/javascript" src="../../_static/js/theme.js"></script>
-
<script type="text/javascript">
jQuery(function () {
SphinxRtdTheme.Navigation.enable(true);
});
- </script>
+ </script>
+
+
+
+
+
</body>
</html>
\ No newline at end of file
diff --git a/doc/_build/html/_modules/jass_preprocessing/map_reference.html b/doc/_build/html/_modules/jass_preprocessing/map_reference.html
index 336b4d01f6c1864fbccce43fdeec165919dcf4ea..3279e2ded5c2e64158a10b9eec98bd84647232fe 100644
--- a/doc/_build/html/_modules/jass_preprocessing/map_reference.html
+++ b/doc/_build/html/_modules/jass_preprocessing/map_reference.html
@@ -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>
+ <script type="text/javascript" src="../../_static/jquery.js"></script>
+ <script type="text/javascript" src="../../_static/underscore.js"></script>
+ <script type="text/javascript" src="../../_static/doctools.js"></script>
+ <script type="text/javascript" src="../../_static/language_data.js"></script>
+
+ <script type="text/javascript" src="../../_static/js/theme.js"></script>
-
+
+
<link rel="stylesheet" href="../../_static/css/theme.css" type="text/css" />
<link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
<link rel="index" title="Index" href="../../genindex.html" />
<link rel="search" title="Search" href="../../search.html" />
-
-
- <script src="../../_static/js/modernizr.min.js"></script>
-
</head>
<body class="wy-body-for-nav">
<div class="wy-grid-for-nav">
-
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
<div class="wy-side-scroll">
- <div class="wy-side-nav-search">
+ <div class="wy-side-nav-search" >
@@ -149,17 +151,37 @@
<span class="kn">import</span> <span class="nn">jass_preprocessing.dna_utils</span> <span class="k">as</span> <span class="nn">dna_u</span>
<span class="kn">import</span> <span class="nn">warnings</span>
-
-<div class="viewcode-block" id="read_reference"><a class="viewcode-back" href="../../_autosummary/jass_preprocessing.html#jass_preprocessing.map_reference.read_reference">[docs]</a><span class="k">def</span> <span class="nf">read_reference</span><span class="p">(</span><span class="n">gwas_reference_panel</span><span class="p">):</span>
+<div class="viewcode-block" id="read_reference"><a class="viewcode-back" href="../../_autosummary/jass_preprocessing.html#jass_preprocessing.map_reference.read_reference">[docs]</a><span class="k">def</span> <span class="nf">read_reference</span><span class="p">(</span><span class="n">gwas_reference_panel</span><span class="p">,</span> <span class="n">mask_MHC</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">minimum_MAF</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">region_to_mask</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> helper function to name correctly the column</span>
+<span class="sd"> Args:</span>
+<span class="sd"> gwas_reference_panel (str): path toward the reference panel file</span>
+<span class="sd"> mask_MHC (bool): Whether the MHC region should be masked or not. default is False</span>
+<span class="sd"> Filter the reference panel by minimum allele frequency (hg19 coordinate)</span>
+<span class="sd"> minimum_MAF (float): minimum allele frequency for a SNPs to be retain in the panel</span>
+<span class="sd"> region_to_mask (dict): a list of additional regions to mask</span>
+<span class="sd"> Return:</span>
+<span class="sd"> ref (pandas dataframe): the reference_panel with the specified filter applied</span>
<span class="sd"> """</span>
- <span class="n">ref</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="n">REF_filename</span><span class="p">,</span> <span class="n">header</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">sep</span><span class="o">=</span> <span class="s2">"</span><span class="se">\t</span><span class="s2">"</span><span class="p">,</span>
+ <span class="n">ref</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="n">gwas_reference_panel</span><span class="p">,</span> <span class="n">header</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">sep</span><span class="o">=</span> <span class="s2">"</span><span class="se">\t</span><span class="s2">"</span><span class="p">,</span>
<span class="n">names</span> <span class="o">=</span><span class="p">[</span><span class="s1">'chr'</span><span class="p">,</span> <span class="s2">"pos"</span><span class="p">,</span> <span class="s2">"snp_id"</span><span class="p">,</span> <span class="s2">"ref"</span><span class="p">,</span> <span class="s2">"alt"</span><span class="p">,</span> <span class="s2">"MAF"</span><span class="p">],</span>
<span class="n">index_col</span><span class="o">=</span><span class="s2">"snp_id"</span><span class="p">)</span>
+ <span class="c1">#Filter Strand ambiguous</span>
+ <span class="n">ref</span> <span class="o">=</span> <span class="n">ref</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="o">~</span><span class="p">(</span><span class="n">ref</span><span class="o">.</span><span class="n">ref</span><span class="o">+</span><span class="n">ref</span><span class="o">.</span><span class="n">alt</span><span class="p">)</span><span class="o">.</span><span class="n">isin</span><span class="p">([</span><span class="s2">"AT"</span><span class="p">,</span> <span class="s2">"TA"</span><span class="p">,</span> <span class="s1">'CG'</span><span class="p">,</span><span class="s1">'GC'</span><span class="p">])]</span>
+
+ <span class="k">if</span> <span class="n">mask_MHC</span><span class="p">:</span>
+ <span class="n">ref</span> <span class="o">=</span> <span class="n">ref</span><span class="o">.</span><span class="n">loc</span><span class="p">[(</span><span class="n">ref</span><span class="o">.</span><span class="n">chr</span> <span class="o">!=</span><span class="mi">6</span><span class="p">)</span><span class="o">|</span><span class="p">(</span><span class="n">ref</span><span class="o">.</span><span class="n">pos</span> <span class="o"><</span> <span class="mi">28477797</span><span class="p">)</span><span class="o">|</span><span class="p">(</span><span class="n">ref</span><span class="o">.</span><span class="n">pos</span> <span class="o">></span> <span class="mi">33448354</span><span class="p">)]</span>
+
+ <span class="k">if</span> <span class="n">minimum_MAF</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">ref</span> <span class="o">=</span> <span class="n">ref</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">ref</span><span class="o">.</span><span class="n">MAF</span> <span class="o">></span> <span class="n">minimum_MAF</span><span class="p">]</span>
+
+ <span class="k">if</span> <span class="n">region_to_mask</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">reg</span> <span class="ow">in</span> <span class="n">region_to_mask</span><span class="p">:</span>
+ <span class="n">ref</span> <span class="o">=</span> <span class="n">ref</span><span class="o">.</span><span class="n">loc</span><span class="p">[(</span><span class="n">ref</span><span class="o">.</span><span class="n">chr</span> <span class="o">!=</span> <span class="n">reg</span><span class="p">[</span><span class="s2">"chr"</span><span class="p">])</span> <span class="o">|</span> <span class="p">(</span><span class="n">ref</span><span class="o">.</span><span class="n">pos</span> <span class="o"><</span><span class="n">reg</span><span class="p">[</span><span class="s2">"start"</span><span class="p">])</span><span class="o">|</span><span class="p">(</span><span class="n">ref</span><span class="o">.</span><span class="n">pos</span> <span class="o">></span> <span class="n">reg</span><span class="p">[</span><span class="s2">"end"</span><span class="p">])]</span>
<span class="k">return</span><span class="p">(</span><span class="n">ref</span><span class="p">)</span></div>
+
<div class="viewcode-block" id="map_on_ref_panel"><a class="viewcode-back" href="../../_autosummary/jass_preprocessing.html#jass_preprocessing.map_reference.map_on_ref_panel">[docs]</a><span class="k">def</span> <span class="nf">map_on_ref_panel</span><span class="p">(</span><span class="n">gw_df</span> <span class="p">,</span> <span class="n">ref_panel</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Merge Gwas dataframe with the reference panel</span>
@@ -294,25 +316,16 @@
-
-
-
-
- <script type="text/javascript" id="documentation_options" data-url_root="../../" src="../../_static/documentation_options.js"></script>
- <script type="text/javascript" src="../../_static/jquery.js"></script>
- <script type="text/javascript" src="../../_static/underscore.js"></script>
- <script type="text/javascript" src="../../_static/doctools.js"></script>
-
-
-
-
- <script type="text/javascript" src="../../_static/js/theme.js"></script>
-
<script type="text/javascript">
jQuery(function () {
SphinxRtdTheme.Navigation.enable(true);
});
- </script>
+ </script>
+
+
+
+
+
</body>
</html>
\ No newline at end of file
diff --git a/doc/_build/html/_modules/jass_preprocessing/save_output.html b/doc/_build/html/_modules/jass_preprocessing/save_output.html
index f9a906ee2fd0c0b6f3ed3d759fc0f70f5463714e..4b47c439e7b90fb787f760230fdf54828bd6241b 100644
--- a/doc/_build/html/_modules/jass_preprocessing/save_output.html
+++ b/doc/_build/html/_modules/jass_preprocessing/save_output.html
@@ -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>
+ <script type="text/javascript" src="../../_static/jquery.js"></script>
+ <script type="text/javascript" src="../../_static/underscore.js"></script>
+ <script type="text/javascript" src="../../_static/doctools.js"></script>
+ <script type="text/javascript" src="../../_static/language_data.js"></script>
+
+ <script type="text/javascript" src="../../_static/js/theme.js"></script>
-
+
+
<link rel="stylesheet" href="../../_static/css/theme.css" type="text/css" />
<link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
<link rel="index" title="Index" href="../../genindex.html" />
<link rel="search" title="Search" href="../../search.html" />
-
-
- <script src="../../_static/js/modernizr.min.js"></script>
-
</head>
<body class="wy-body-for-nav">
<div class="wy-grid-for-nav">
-
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
<div class="wy-side-scroll">
- <div class="wy-side-nav-search">
+ <div class="wy-side-nav-search" >
@@ -217,25 +219,16 @@
-
-
-
-
- <script type="text/javascript" id="documentation_options" data-url_root="../../" src="../../_static/documentation_options.js"></script>
- <script type="text/javascript" src="../../_static/jquery.js"></script>
- <script type="text/javascript" src="../../_static/underscore.js"></script>
- <script type="text/javascript" src="../../_static/doctools.js"></script>
-
-
-
-
- <script type="text/javascript" src="../../_static/js/theme.js"></script>
-
<script type="text/javascript">
jQuery(function () {
SphinxRtdTheme.Navigation.enable(true);
});
- </script>
+ </script>
+
+
+
+
+
</body>
</html>
\ No newline at end of file
diff --git a/doc/_build/html/_sources/index.rst.txt b/doc/_build/html/_sources/index.rst.txt
index 733fd0b36cef188589dd8826d06ac14a421f42ea..83387d811424fce8607e4741070f08c1c1c48550 100644
--- a/doc/_build/html/_sources/index.rst.txt
+++ b/doc/_build/html/_sources/index.rst.txt
@@ -70,7 +70,7 @@ Input
| 1 |14930| rs75454623 | A | G | 0.482228|
+-----+-----+------------+-----+-----+---------+
-* Folder containing all raw gwas data (all chromosomes in one file) (minimal conditions?? tab separated?)
+* Folder containing all raw gwas data : (all chromosomes in one file) (minimal conditions?? tab separated?)
* a list containing the name of GWAS file to the string format.
* A descriptor csv files that will described each GWAS summary statistic files:
@@ -84,7 +84,7 @@ Input
+===========================================+============================================================+
| path to the data | filename |
+-------------------------------------------+------------------------------------------------------------+
-| study info fields | consortia,outcome,fullName,type,Nsample,Ncase,Ncontrol,Nsnp|
+| study info fields | Consortium,Outcome,fullName,type,Nsample,Ncase,Ncontrol,Nsnp|
+-------------------------------------------+------------------------------------------------------------+
| names of the header in the GWAS file | snpid,a1,a2,freq,pval,n,z,OR,se,code,imp,ncas,ncont |
+-------------------------------------------+------------------------------------------------------------+
@@ -92,6 +92,7 @@ Input
.. Give an example
.. | I don't know | altNcas,altNcont|
+Note that the combination of Consortium and outcome must be unique because it will be used as an index in the cleaning process.
Here is an example of descriptor field, the field irrelevant (for example odd ratio for continuous trait) for the study must be filled with na.
diff --git a/doc/_build/html/_static/basic.css b/doc/_build/html/_static/basic.css
index 104f076ae8ae5d6118dc13db6cb16e2ae9de1bda..ea6972d55273ba89dd060c362ed5662aa53049dd 100644
--- a/doc/_build/html/_static/basic.css
+++ b/doc/_build/html/_static/basic.css
@@ -4,7 +4,7 @@
*
* Sphinx stylesheet -- basic theme.
*
- * :copyright: Copyright 2007-2018 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2019 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
@@ -231,6 +231,16 @@ a.headerlink {
visibility: hidden;
}
+a.brackets:before,
+span.brackets > a:before{
+ content: "[";
+}
+
+a.brackets:after,
+span.brackets > a:after {
+ content: "]";
+}
+
h1:hover > a.headerlink,
h2:hover > a.headerlink,
h3:hover > a.headerlink,
@@ -279,6 +289,12 @@ img.align-center, .figure.align-center, object.align-center {
margin-right: auto;
}
+img.align-default, .figure.align-default {
+ display: block;
+ margin-left: auto;
+ margin-right: auto;
+}
+
.align-left {
text-align: left;
}
@@ -287,6 +303,10 @@ img.align-center, .figure.align-center, object.align-center {
text-align: center;
}
+.align-default {
+ text-align: center;
+}
+
.align-right {
text-align: right;
}
@@ -358,6 +378,11 @@ table.align-center {
margin-right: auto;
}
+table.align-default {
+ margin-left: auto;
+ margin-right: auto;
+}
+
table caption span.caption-number {
font-style: italic;
}
@@ -391,6 +416,16 @@ table.citation td {
border-bottom: none;
}
+th > p:first-child,
+td > p:first-child {
+ margin-top: 0px;
+}
+
+th > p:last-child,
+td > p:last-child {
+ margin-bottom: 0px;
+}
+
/* -- figures --------------------------------------------------------------- */
div.figure {
@@ -460,11 +495,58 @@ ol.upperroman {
list-style: upper-roman;
}
+li > p:first-child {
+ margin-top: 0px;
+}
+
+li > p:last-child {
+ margin-bottom: 0px;
+}
+
+dl.footnote > dt,
+dl.citation > dt {
+ float: left;
+}
+
+dl.footnote > dd,
+dl.citation > dd {
+ margin-bottom: 0em;
+}
+
+dl.footnote > dd:after,
+dl.citation > dd:after {
+ content: "";
+ clear: both;
+}
+
+dl.field-list {
+ display: grid;
+ grid-template-columns: fit-content(30%) auto;
+}
+
+dl.field-list > dt {
+ font-weight: bold;
+ word-break: break-word;
+ padding-left: 0.5em;
+ padding-right: 5px;
+}
+
+dl.field-list > dt:after {
+ content: ":";
+}
+
+dl.field-list > dd {
+ padding-left: 0.5em;
+ margin-top: 0em;
+ margin-left: 0em;
+ margin-bottom: 0em;
+}
+
dl {
margin-bottom: 15px;
}
-dd p {
+dd > p:first-child {
margin-top: 0px;
}
@@ -537,6 +619,12 @@ dl.glossary dt {
font-style: oblique;
}
+.classifier:before {
+ font-style: normal;
+ margin: 0.5em;
+ content: ":";
+}
+
abbr, acronym {
border-bottom: dotted 1px;
cursor: help;
diff --git a/doc/_build/html/_static/doctools.js b/doc/_build/html/_static/doctools.js
index ffadbec11f71c338696d5c014de9b64afe31a516..b33f87fcb249ea9b0e0a07fa9c5f2595ea925709 100644
--- a/doc/_build/html/_static/doctools.js
+++ b/doc/_build/html/_static/doctools.js
@@ -4,7 +4,7 @@
*
* Sphinx JavaScript utilities for all documentation.
*
- * :copyright: Copyright 2007-2018 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2019 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
@@ -87,14 +87,13 @@ jQuery.fn.highlightText = function(text, className) {
node.nextSibling));
node.nodeValue = val.substr(0, pos);
if (isInSVG) {
- var bbox = span.getBBox();
var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect");
- rect.x.baseVal.value = bbox.x;
+ var bbox = node.parentElement.getBBox();
+ rect.x.baseVal.value = bbox.x;
rect.y.baseVal.value = bbox.y;
rect.width.baseVal.value = bbox.width;
rect.height.baseVal.value = bbox.height;
rect.setAttribute('class', className);
- var parentOfText = node.parentNode.parentNode;
addItems.push({
"parent": node.parentNode,
"target": rect});
diff --git a/doc/_build/html/_static/documentation_options.js b/doc/_build/html/_static/documentation_options.js
index 837eacf30de116b6aff70d9761453e9c93abb1b5..ad3a3d9951050f3fd099b523db3c945db6691c36 100644
--- a/doc/_build/html/_static/documentation_options.js
+++ b/doc/_build/html/_static/documentation_options.js
@@ -6,291 +6,5 @@ var DOCUMENTATION_OPTIONS = {
FILE_SUFFIX: '.html',
HAS_SOURCE: true,
SOURCELINK_SUFFIX: '.txt',
- NAVIGATION_WITH_KEYS: false,
- SEARCH_LANGUAGE_STOP_WORDS: ["a","and","are","as","at","be","but","by","for","if","in","into","is","it","near","no","not","of","on","or","such","that","the","their","then","there","these","they","this","to","was","will","with"]
-};
-
-
-
-/* Non-minified version JS is _stemmer.js if file is provided */
-/**
- * Porter Stemmer
- */
-var Stemmer = function() {
-
- var step2list = {
- ational: 'ate',
- tional: 'tion',
- enci: 'ence',
- anci: 'ance',
- izer: 'ize',
- bli: 'ble',
- alli: 'al',
- entli: 'ent',
- eli: 'e',
- ousli: 'ous',
- ization: 'ize',
- ation: 'ate',
- ator: 'ate',
- alism: 'al',
- iveness: 'ive',
- fulness: 'ful',
- ousness: 'ous',
- aliti: 'al',
- iviti: 'ive',
- biliti: 'ble',
- logi: 'log'
- };
-
- var step3list = {
- icate: 'ic',
- ative: '',
- alize: 'al',
- iciti: 'ic',
- ical: 'ic',
- ful: '',
- ness: ''
- };
-
- var c = "[^aeiou]"; // consonant
- var v = "[aeiouy]"; // vowel
- var C = c + "[^aeiouy]*"; // consonant sequence
- var V = v + "[aeiou]*"; // vowel sequence
-
- var mgr0 = "^(" + C + ")?" + V + C; // [C]VC... is m>0
- var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$"; // [C]VC[V] is m=1
- var mgr1 = "^(" + C + ")?" + V + C + V + C; // [C]VCVC... is m>1
- var s_v = "^(" + C + ")?" + v; // vowel in stem
-
- this.stemWord = function (w) {
- var stem;
- var suffix;
- var firstch;
- var origword = w;
-
- if (w.length < 3)
- return w;
-
- var re;
- var re2;
- var re3;
- var re4;
-
- firstch = w.substr(0,1);
- if (firstch == "y")
- w = firstch.toUpperCase() + w.substr(1);
-
- // Step 1a
- re = /^(.+?)(ss|i)es$/;
- re2 = /^(.+?)([^s])s$/;
-
- if (re.test(w))
- w = w.replace(re,"$1$2");
- else if (re2.test(w))
- w = w.replace(re2,"$1$2");
-
- // Step 1b
- re = /^(.+?)eed$/;
- re2 = /^(.+?)(ed|ing)$/;
- if (re.test(w)) {
- var fp = re.exec(w);
- re = new RegExp(mgr0);
- if (re.test(fp[1])) {
- re = /.$/;
- w = w.replace(re,"");
- }
- }
- else if (re2.test(w)) {
- var fp = re2.exec(w);
- stem = fp[1];
- re2 = new RegExp(s_v);
- if (re2.test(stem)) {
- w = stem;
- re2 = /(at|bl|iz)$/;
- re3 = new RegExp("([^aeiouylsz])\\1$");
- re4 = new RegExp("^" + C + v + "[^aeiouwxy]$");
- if (re2.test(w))
- w = w + "e";
- else if (re3.test(w)) {
- re = /.$/;
- w = w.replace(re,"");
- }
- else if (re4.test(w))
- w = w + "e";
- }
- }
-
- // Step 1c
- re = /^(.+?)y$/;
- if (re.test(w)) {
- var fp = re.exec(w);
- stem = fp[1];
- re = new RegExp(s_v);
- if (re.test(stem))
- w = stem + "i";
- }
-
- // Step 2
- re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/;
- if (re.test(w)) {
- var fp = re.exec(w);
- stem = fp[1];
- suffix = fp[2];
- re = new RegExp(mgr0);
- if (re.test(stem))
- w = stem + step2list[suffix];
- }
-
- // Step 3
- re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/;
- if (re.test(w)) {
- var fp = re.exec(w);
- stem = fp[1];
- suffix = fp[2];
- re = new RegExp(mgr0);
- if (re.test(stem))
- w = stem + step3list[suffix];
- }
-
- // Step 4
- re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/;
- re2 = /^(.+?)(s|t)(ion)$/;
- if (re.test(w)) {
- var fp = re.exec(w);
- stem = fp[1];
- re = new RegExp(mgr1);
- if (re.test(stem))
- w = stem;
- }
- else if (re2.test(w)) {
- var fp = re2.exec(w);
- stem = fp[1] + fp[2];
- re2 = new RegExp(mgr1);
- if (re2.test(stem))
- w = stem;
- }
-
- // Step 5
- re = /^(.+?)e$/;
- if (re.test(w)) {
- var fp = re.exec(w);
- stem = fp[1];
- re = new RegExp(mgr1);
- re2 = new RegExp(meq1);
- re3 = new RegExp("^" + C + v + "[^aeiouwxy]$");
- if (re.test(stem) || (re2.test(stem) && !(re3.test(stem))))
- w = stem;
- }
- re = /ll$/;
- re2 = new RegExp(mgr1);
- if (re.test(w) && re2.test(w)) {
- re = /.$/;
- w = w.replace(re,"");
- }
-
- // and turn initial Y back to y
- if (firstch == "y")
- w = firstch.toLowerCase() + w.substr(1);
- return w;
- }
-}
-
-
-
-
-
-var splitChars = (function() {
- var result = {};
- var singles = [96, 180, 187, 191, 215, 247, 749, 885, 903, 907, 909, 930, 1014, 1648,
- 1748, 1809, 2416, 2473, 2481, 2526, 2601, 2609, 2612, 2615, 2653, 2702,
- 2706, 2729, 2737, 2740, 2857, 2865, 2868, 2910, 2928, 2948, 2961, 2971,
- 2973, 3085, 3089, 3113, 3124, 3213, 3217, 3241, 3252, 3295, 3341, 3345,
- 3369, 3506, 3516, 3633, 3715, 3721, 3736, 3744, 3748, 3750, 3756, 3761,
- 3781, 3912, 4239, 4347, 4681, 4695, 4697, 4745, 4785, 4799, 4801, 4823,
- 4881, 5760, 5901, 5997, 6313, 7405, 8024, 8026, 8028, 8030, 8117, 8125,
- 8133, 8181, 8468, 8485, 8487, 8489, 8494, 8527, 11311, 11359, 11687, 11695,
- 11703, 11711, 11719, 11727, 11735, 12448, 12539, 43010, 43014, 43019, 43587,
- 43696, 43713, 64286, 64297, 64311, 64317, 64319, 64322, 64325, 65141];
- var i, j, start, end;
- for (i = 0; i < singles.length; i++) {
- result[singles[i]] = true;
- }
- var ranges = [[0, 47], [58, 64], [91, 94], [123, 169], [171, 177], [182, 184], [706, 709],
- [722, 735], [741, 747], [751, 879], [888, 889], [894, 901], [1154, 1161],
- [1318, 1328], [1367, 1368], [1370, 1376], [1416, 1487], [1515, 1519], [1523, 1568],
- [1611, 1631], [1642, 1645], [1750, 1764], [1767, 1773], [1789, 1790], [1792, 1807],
- [1840, 1868], [1958, 1968], [1970, 1983], [2027, 2035], [2038, 2041], [2043, 2047],
- [2070, 2073], [2075, 2083], [2085, 2087], [2089, 2307], [2362, 2364], [2366, 2383],
- [2385, 2391], [2402, 2405], [2419, 2424], [2432, 2436], [2445, 2446], [2449, 2450],
- [2483, 2485], [2490, 2492], [2494, 2509], [2511, 2523], [2530, 2533], [2546, 2547],
- [2554, 2564], [2571, 2574], [2577, 2578], [2618, 2648], [2655, 2661], [2672, 2673],
- [2677, 2692], [2746, 2748], [2750, 2767], [2769, 2783], [2786, 2789], [2800, 2820],
- [2829, 2830], [2833, 2834], [2874, 2876], [2878, 2907], [2914, 2917], [2930, 2946],
- [2955, 2957], [2966, 2968], [2976, 2978], [2981, 2983], [2987, 2989], [3002, 3023],
- [3025, 3045], [3059, 3076], [3130, 3132], [3134, 3159], [3162, 3167], [3170, 3173],
- [3184, 3191], [3199, 3204], [3258, 3260], [3262, 3293], [3298, 3301], [3312, 3332],
- [3386, 3388], [3390, 3423], [3426, 3429], [3446, 3449], [3456, 3460], [3479, 3481],
- [3518, 3519], [3527, 3584], [3636, 3647], [3655, 3663], [3674, 3712], [3717, 3718],
- [3723, 3724], [3726, 3731], [3752, 3753], [3764, 3772], [3774, 3775], [3783, 3791],
- [3802, 3803], [3806, 3839], [3841, 3871], [3892, 3903], [3949, 3975], [3980, 4095],
- [4139, 4158], [4170, 4175], [4182, 4185], [4190, 4192], [4194, 4196], [4199, 4205],
- [4209, 4212], [4226, 4237], [4250, 4255], [4294, 4303], [4349, 4351], [4686, 4687],
- [4702, 4703], [4750, 4751], [4790, 4791], [4806, 4807], [4886, 4887], [4955, 4968],
- [4989, 4991], [5008, 5023], [5109, 5120], [5741, 5742], [5787, 5791], [5867, 5869],
- [5873, 5887], [5906, 5919], [5938, 5951], [5970, 5983], [6001, 6015], [6068, 6102],
- [6104, 6107], [6109, 6111], [6122, 6127], [6138, 6159], [6170, 6175], [6264, 6271],
- [6315, 6319], [6390, 6399], [6429, 6469], [6510, 6511], [6517, 6527], [6572, 6592],
- [6600, 6607], [6619, 6655], [6679, 6687], [6741, 6783], [6794, 6799], [6810, 6822],
- [6824, 6916], [6964, 6980], [6988, 6991], [7002, 7042], [7073, 7085], [7098, 7167],
- [7204, 7231], [7242, 7244], [7294, 7400], [7410, 7423], [7616, 7679], [7958, 7959],
- [7966, 7967], [8006, 8007], [8014, 8015], [8062, 8063], [8127, 8129], [8141, 8143],
- [8148, 8149], [8156, 8159], [8173, 8177], [8189, 8303], [8306, 8307], [8314, 8318],
- [8330, 8335], [8341, 8449], [8451, 8454], [8456, 8457], [8470, 8472], [8478, 8483],
- [8506, 8507], [8512, 8516], [8522, 8525], [8586, 9311], [9372, 9449], [9472, 10101],
- [10132, 11263], [11493, 11498], [11503, 11516], [11518, 11519], [11558, 11567],
- [11622, 11630], [11632, 11647], [11671, 11679], [11743, 11822], [11824, 12292],
- [12296, 12320], [12330, 12336], [12342, 12343], [12349, 12352], [12439, 12444],
- [12544, 12548], [12590, 12592], [12687, 12689], [12694, 12703], [12728, 12783],
- [12800, 12831], [12842, 12880], [12896, 12927], [12938, 12976], [12992, 13311],
- [19894, 19967], [40908, 40959], [42125, 42191], [42238, 42239], [42509, 42511],
- [42540, 42559], [42592, 42593], [42607, 42622], [42648, 42655], [42736, 42774],
- [42784, 42785], [42889, 42890], [42893, 43002], [43043, 43055], [43062, 43071],
- [43124, 43137], [43188, 43215], [43226, 43249], [43256, 43258], [43260, 43263],
- [43302, 43311], [43335, 43359], [43389, 43395], [43443, 43470], [43482, 43519],
- [43561, 43583], [43596, 43599], [43610, 43615], [43639, 43641], [43643, 43647],
- [43698, 43700], [43703, 43704], [43710, 43711], [43715, 43738], [43742, 43967],
- [44003, 44015], [44026, 44031], [55204, 55215], [55239, 55242], [55292, 55295],
- [57344, 63743], [64046, 64047], [64110, 64111], [64218, 64255], [64263, 64274],
- [64280, 64284], [64434, 64466], [64830, 64847], [64912, 64913], [64968, 65007],
- [65020, 65135], [65277, 65295], [65306, 65312], [65339, 65344], [65371, 65381],
- [65471, 65473], [65480, 65481], [65488, 65489], [65496, 65497]];
- for (i = 0; i < ranges.length; i++) {
- start = ranges[i][0];
- end = ranges[i][1];
- for (j = start; j <= end; j++) {
- result[j] = true;
- }
- }
- return result;
-})();
-
-function splitQuery(query) {
- var result = [];
- var start = -1;
- for (var i = 0; i < query.length; i++) {
- if (splitChars[query.charCodeAt(i)]) {
- if (start !== -1) {
- result.push(query.slice(start, i));
- start = -1;
- }
- } else if (start === -1) {
- start = i;
- }
- }
- if (start !== -1) {
- result.push(query.slice(start));
- }
- return result;
-}
-
-
+ NAVIGATION_WITH_KEYS: false
+};
\ No newline at end of file
diff --git a/doc/_build/html/_static/jquery.js b/doc/_build/html/_static/jquery.js
index 644d35e274fd64ddaf6d12af813e820c424176a9..a1c07fd803b5fc9c54f44e31123ae4fa11e134b0 100644
--- a/doc/_build/html/_static/jquery.js
+++ b/doc/_build/html/_static/jquery.js
@@ -1,4 +1,2 @@
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i&&(o=e,e=i,i=void 0),e&&!1!==i&&this.queue(i||"fx",[]),this.each(function(){var e=!0,t=null!=i&&i+"queueHooks",n=k.timers,r=Q.get(this);if(t)r[t]&&r[t].stop&&a(r[t]);else for(t in r)r[t]&&r[t].stop&&ut.test(t)&&a(r[t]);for(t=n.length;t--;)n[t].elem!==this||null!=i&&n[t].queue!==i||(n[t].anim.stop(o),e=!1,n.splice(t,1));!e&&o||k.dequeue(this,i)})},finish:function(a){return!1!==a&&(a=a||"fx"),this.each(function(){var e,t=Q.get(this),n=t[a+"queue"],r=t[a+"queueHooks"],i=k.timers,o=n?n.length:0;for(t.finish=!0,k.queue(this,a,[]),r&&r.stop&&r.stop.call(this,!0),e=i.length;e--;)i[e].elem===this&&i[e].queue===a&&(i[e].anim.stop(!0),i.splice(e,1));for(e=0;e<o;e++)n[e]&&n[e].finish&&n[e].finish.call(this);delete t.finish})}}),k.each(["toggle","show","hide"],function(e,r){var i=k.fn[r];k.fn[r]=function(e,t,n){return null==e||"boolean"==typeof e?i.apply(this,arguments):this.animate(ft(r,!0),e,t,n)}}),k.each({slideDown:ft("show"),slideUp:ft("hide"),slideToggle:ft("toggle"),fadeIn:{opacity:"show"},fadeOut:{opacity:"hide"},fadeToggle:{opacity:"toggle"}},function(e,r){k.fn[e]=function(e,t,n){return this.animate(r,e,t,n)}}),k.timers=[],k.fx.tick=function(){var e,t=0,n=k.timers;for(rt=Date.now();t<n.length;t++)(e=n[t])()||n[t]!==e||n.splice(t--,1);n.length||k.fx.stop(),rt=void 0},k.fx.timer=function(e){k.timers.push(e),k.fx.start()},k.fx.interval=13,k.fx.start=function(){it||(it=!0,lt())},k.fx.stop=function(){it=null},k.fx.speeds={slow:600,fast:200,_default:400},k.fn.delay=function(r,e){return r=k.fx&&k.fx.speeds[r]||r,e=e||"fx",this.queue(e,function(e,t){var n=C.setTimeout(e,r);t.stop=function(){C.clearTimeout(n)}})},ot=E.createElement("input"),at=E.createElement("select").appendChild(E.createElement("option")),ot.type="checkbox",y.checkOn=""!==ot.value,y.optSelected=at.selected,(ot=E.createElement("input")).value="t",ot.type="radio",y.radioValue="t"===ot.value;var ht,gt=k.expr.attrHandle;k.fn.extend({attr:function(e,t){return _(this,k.attr,e,t,1<arguments.length)},removeAttr:function(e){return this.each(function(){k.removeAttr(this,e)})}}),k.extend({attr:function(e,t,n){var r,i,o=e.nodeType;if(3!==o&&8!==o&&2!==o)return"undefined"==typeof e.getAttribute?k.prop(e,t,n):(1===o&&k.isXMLDoc(e)||(i=k.attrHooks[t.toLowerCase()]||(k.expr.match.bool.test(t)?ht:void 0)),void 0!==n?null===n?void k.removeAttr(e,t):i&&"set"in i&&void 0!==(r=i.set(e,n,t))?r:(e.setAttribute(t,n+""),n):i&&"get"in i&&null!==(r=i.get(e,t))?r:null==(r=k.find.attr(e,t))?void 0:r)},attrHooks:{type:{set:function(e,t){if(!y.radioValue&&"radio"===t&&A(e,"input")){var n=e.value;return e.setAttribute("type",t),n&&(e.value=n),t}}}},removeAttr:function(e,t){var n,r=0,i=t&&t.match(R);if(i&&1===e.nodeType)while(n=i[r++])e.removeAttribute(n)}}),ht={set:function(e,t,n){return!1===t?k.removeAttr(e,n):e.setAttribute(n,n),n}},k.each(k.expr.match.bool.source.match(/\w+/g),function(e,t){var a=gt[t]||k.find.attr;gt[t]=function(e,t,n){var r,i,o=t.toLowerCase();return n||(i=gt[o],gt[o]=r,r=null!=a(e,t,n)?o:null,gt[o]=i),r}});var vt=/^(?:input|select|textarea|button)$/i,yt=/^(?:a|area)$/i;function mt(e){return(e.match(R)||[]).join(" ")}function xt(e){return e.getAttribute&&e.getAttribute("class")||""}function bt(e){return Array.isArray(e)?e:"string"==typeof e&&e.match(R)||[]}k.fn.extend({prop:function(e,t){return _(this,k.prop,e,t,1<arguments.length)},removeProp:function(e){return this.each(function(){delete this[k.propFix[e]||e]})}}),k.extend({prop:function(e,t,n){var r,i,o=e.nodeType;if(3!==o&&8!==o&&2!==o)return 1===o&&k.isXMLDoc(e)||(t=k.propFix[t]||t,i=k.propHooks[t]),void 0!==n?i&&"set"in i&&void 0!==(r=i.set(e,n,t))?r:e[t]=n:i&&"get"in i&&null!==(r=i.get(e,t))?r:e[t]},propHooks:{tabIndex:{get:function(e){var t=k.find.attr(e,"tabindex");return t?parseInt(t,10):vt.test(e.nodeName)||yt.test(e.nodeName)&&e.href?0:-1}}},propFix:{"for":"htmlFor","class":"className"}}),y.optSelected||(k.propHooks.selected={get:function(e){var t=e.parentNode;return t&&t.parentNode&&t.parentNode.selectedIndex,null},set:function(e){var t=e.parentNode;t&&(t.selectedIndex,t.parentNode&&t.parentNode.selectedIndex)}}),k.each(["tabIndex","readOnly","maxLength","cellSpacing","cellPadding","rowSpan","colSpan","useMap","frameBorder","contentEditable"],function(){k.propFix[this.toLowerCase()]=this}),k.fn.extend({addClass:function(t){var e,n,r,i,o,a,s,u=0;if(m(t))return this.each(function(e){k(this).addClass(t.call(this,e,xt(this)))});if((e=bt(t)).length)while(n=this[u++])if(i=xt(n),r=1===n.nodeType&&" "+mt(i)+" 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null!=t?t:mt(k.text(e))}},select:{get:function(e){var t,n,r,i=e.options,o=e.selectedIndex,a="select-one"===e.type,s=a?null:[],u=a?o+1:i.length;for(r=o<0?u:a?o:0;r<u;r++)if(((n=i[r]).selected||r===o)&&!n.disabled&&(!n.parentNode.disabled||!A(n.parentNode,"optgroup"))){if(t=k(n).val(),a)return t;s.push(t)}return s},set:function(e,t){var n,r,i=e.options,o=k.makeArray(t),a=i.length;while(a--)((r=i[a]).selected=-1<k.inArray(k.valHooks.option.get(r),o))&&(n=!0);return n||(e.selectedIndex=-1),o}}}}),k.each(["radio","checkbox"],function(){k.valHooks[this]={set:function(e,t){if(Array.isArray(t))return e.checked=-1<k.inArray(k(e).val(),t)}},y.checkOn||(k.valHooks[this].get=function(e){return null===e.getAttribute("value")?"on":e.value})}),y.focusin="onfocusin"in C;var Tt=/^(?:focusinfocus|focusoutblur)$/,Ct=function(e){e.stopPropagation()};k.extend(k.event,{trigger:function(e,t,n,r){var i,o,a,s,u,l,c,f,p=[n||E],d=v.call(e,"type")?e.type:e,h=v.call(e,"namespace")?e.namespace.split("."):[];if(o=f=a=n=n||E,3!==n.nodeType&&8!==n.nodeType&&!Tt.test(d+k.event.triggered)&&(-1<d.indexOf(".")&&(d=(h=d.split(".")).shift(),h.sort()),u=d.indexOf(":")<0&&"on"+d,(e=e[k.expando]?e:new k.Event(d,"object"==typeof e&&e)).isTrigger=r?2:3,e.namespace=h.join("."),e.rnamespace=e.namespace?new RegExp("(^|\\.)"+h.join("\\.(?:.*\\.|)")+"(\\.|$)"):null,e.result=void 0,e.target||(e.target=n),t=null==t?[e]:k.makeArray(t,[e]),c=k.event.special[d]||{},r||!c.trigger||!1!==c.trigger.apply(n,t))){if(!r&&!c.noBubble&&!x(n)){for(s=c.delegateType||d,Tt.test(s+d)||(o=o.parentNode);o;o=o.parentNode)p.push(o),a=o;a===(n.ownerDocument||E)&&p.push(a.defaultView||a.parentWindow||C)}i=0;while((o=p[i++])&&!e.isPropagationStopped())f=o,e.type=1<i?s:c.bindType||d,(l=(Q.get(o,"events")||{})[e.type]&&Q.get(o,"handle"))&&l.apply(o,t),(l=u&&o[u])&&l.apply&&G(o)&&(e.result=l.apply(o,t),!1===e.result&&e.preventDefault());return e.type=d,r||e.isDefaultPrevented()||c._default&&!1!==c._default.apply(p.pop(),t)||!G(n)||u&&m(n[d])&&!x(n)&&((a=n[u])&&(n[u]=null),k.event.triggered=d,e.isPropagationStopped()&&f.addEventListener(d,Ct),n[d](),e.isPropagationStopped()&&f.removeEventListener(d,Ct),k.event.triggered=void 0,a&&(n[u]=a)),e.result}},simulate:function(e,t,n){var r=k.extend(new 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diff --git a/doc/_build/html/_static/searchtools.js b/doc/_build/html/_static/searchtools.js
index 7473859b245fa63f5d8812e2249c8d1ae67425fd..6031f991319e4a258c6aba6ad0512fd7b91fe5cb 100644
--- a/doc/_build/html/_static/searchtools.js
+++ b/doc/_build/html/_static/searchtools.js
@@ -4,7 +4,7 @@
*
* Sphinx JavaScript utilities for the full-text search.
*
- * :copyright: Copyright 2007-2018 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2019 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
@@ -36,8 +36,10 @@ if (!Scorer) {
// query found in title
title: 15,
+ partialTitle: 7,
// query found in terms
- term: 5
+ term: 5,
+ partialTerm: 2
};
}
@@ -56,6 +58,14 @@ var Search = {
_queued_query : null,
_pulse_status : -1,
+ htmlToText : function(htmlString) {
+ var htmlElement = document.createElement('span');
+ htmlElement.innerHTML = htmlString;
+ $(htmlElement).find('.headerlink').remove();
+ docContent = $(htmlElement).find('[role=main]')[0];
+ return docContent.textContent || docContent.innerText;
+ },
+
init : function() {
var params = $.getQueryParameters();
if (params.q) {
@@ -120,7 +130,7 @@ var Search = {
this.out = $('#search-results');
this.title = $('<h2>' + _('Searching') + '</h2>').appendTo(this.out);
this.dots = $('<span></span>').appendTo(this.title);
- this.status = $('<p style="display: none"></p>').appendTo(this.out);
+ this.status = $('<p class="search-summary"> </p>').appendTo(this.out);
this.output = $('<ul class="search"/>').appendTo(this.out);
$('#search-progress').text(_('Preparing search...'));
@@ -138,7 +148,6 @@ var Search = {
*/
query : function(query) {
var i;
- var stopwords = DOCUMENTATION_OPTIONS.SEARCH_LANGUAGE_STOP_WORDS;
// stem the searchterms and add them to the correct list
var stemmer = new Stemmer();
@@ -260,11 +269,7 @@ var Search = {
displayNextItem();
});
} else if (DOCUMENTATION_OPTIONS.HAS_SOURCE) {
- var suffix = DOCUMENTATION_OPTIONS.SOURCELINK_SUFFIX;
- if (suffix === undefined) {
- suffix = '.txt';
- }
- $.ajax({url: DOCUMENTATION_OPTIONS.URL_ROOT + '_sources/' + item[5] + (item[5].slice(-suffix.length) === suffix ? '' : suffix),
+ $.ajax({url: DOCUMENTATION_OPTIONS.URL_ROOT + item[0] + DOCUMENTATION_OPTIONS.FILE_SUFFIX,
dataType: "text",
complete: function(jqxhr, textstatus) {
var data = jqxhr.responseText;
@@ -314,12 +319,13 @@ var Search = {
for (var prefix in objects) {
for (var name in objects[prefix]) {
var fullname = (prefix ? prefix + '.' : '') + name;
- if (fullname.toLowerCase().indexOf(object) > -1) {
+ var fullnameLower = fullname.toLowerCase()
+ if (fullnameLower.indexOf(object) > -1) {
var score = 0;
- var parts = fullname.split('.');
+ var parts = fullnameLower.split('.');
// check for different match types: exact matches of full name or
// "last name" (i.e. last dotted part)
- if (fullname == object || parts[parts.length - 1] == object) {
+ if (fullnameLower == object || parts[parts.length - 1] == object) {
score += Scorer.objNameMatch;
// matches in last name
} else if (parts[parts.length - 1].indexOf(object) > -1) {
@@ -386,6 +392,19 @@ var Search = {
{files: terms[word], score: Scorer.term},
{files: titleterms[word], score: Scorer.title}
];
+ // add support for partial matches
+ if (word.length > 2) {
+ for (var w in terms) {
+ if (w.match(word) && !terms[word]) {
+ _o.push({files: terms[w], score: Scorer.partialTerm})
+ }
+ }
+ for (var w in titleterms) {
+ if (w.match(word) && !titleterms[word]) {
+ _o.push({files: titleterms[w], score: Scorer.partialTitle})
+ }
+ }
+ }
// no match but word was a required one
if ($u.every(_o, function(o){return o.files === undefined;})) {
@@ -425,8 +444,12 @@ var Search = {
var valid = true;
// check if all requirements are matched
- if (fileMap[file].length != searchterms.length)
- continue;
+ var filteredTermCount = // as search terms with length < 3 are discarded: ignore
+ searchterms.filter(function(term){return term.length > 2}).length
+ if (
+ fileMap[file].length != searchterms.length &&
+ fileMap[file].length != filteredTermCount
+ ) continue;
// ensure that none of the excluded terms is in the search result
for (i = 0; i < excluded.length; i++) {
@@ -457,7 +480,8 @@ var Search = {
* words. the first one is used to find the occurrence, the
* latter for highlighting it.
*/
- makeSearchSummary : function(text, keywords, hlwords) {
+ makeSearchSummary : function(htmlText, keywords, hlwords) {
+ var text = Search.htmlToText(htmlText);
var textLower = text.toLowerCase();
var start = 0;
$.each(keywords, function() {
diff --git a/doc/_build/html/genindex.html b/doc/_build/html/genindex.html
index aa1da30101863920b3e9f57a1df961575fdf94dd..7ec4d12417f0b49a82be730bee4f55a031ab7057 100644
--- a/doc/_build/html/genindex.html
+++ b/doc/_build/html/genindex.html
@@ -18,32 +18,34 @@
-
-
+ <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>
+ <script type="text/javascript" src="_static/jquery.js"></script>
+ <script type="text/javascript" src="_static/underscore.js"></script>
+ <script type="text/javascript" src="_static/doctools.js"></script>
+ <script type="text/javascript" src="_static/language_data.js"></script>
+
+ <script type="text/javascript" src="_static/js/theme.js"></script>
-
+
+
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<link rel="index" title="Index" href="#" />
<link rel="search" title="Search" href="search.html" />
-
-
- <script src="_static/js/modernizr.min.js"></script>
-
</head>
<body class="wy-body-for-nav">
<div class="wy-grid-for-nav">
-
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
<div class="wy-side-scroll">
- <div class="wy-side-nav-search">
+ <div class="wy-side-nav-search" >
@@ -146,7 +148,6 @@
<a href="#C"><strong>C</strong></a>
| <a href="#D"><strong>D</strong></a>
| <a href="#G"><strong>G</strong></a>
- | <a href="#I"><strong>I</strong></a>
| <a href="#J"><strong>J</strong></a>
| <a href="#M"><strong>M</strong></a>
| <a href="#R"><strong>R</strong></a>
@@ -194,14 +195,6 @@
</ul></td>
</tr></table>
-<h2 id="I">I</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
- <td style="width: 33%; vertical-align: top;"><ul>
- <li><a href="index.html#module-impute_jass">impute_jass (module)</a>
-</li>
- </ul></td>
-</tr></table>
-
<h2 id="J">J</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
@@ -295,25 +288,16 @@
-
-
-
-
- <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
- <script type="text/javascript" src="_static/jquery.js"></script>
- <script type="text/javascript" src="_static/underscore.js"></script>
- <script type="text/javascript" src="_static/doctools.js"></script>
-
-
-
-
- <script type="text/javascript" src="_static/js/theme.js"></script>
-
<script type="text/javascript">
jQuery(function () {
SphinxRtdTheme.Navigation.enable(true);
});
- </script>
+ </script>
+
+
+
+
+
</body>
</html>
\ No newline at end of file
diff --git a/doc/_build/html/index.html b/doc/_build/html/index.html
index d124afb3069da18a5b06ba4684faa0fc958012f2..0e893cadb0a3f55a886fe8095b8deac35646e149 100644
--- a/doc/_build/html/index.html
+++ b/doc/_build/html/index.html
@@ -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>
+ <script type="text/javascript" src="_static/jquery.js"></script>
+ <script type="text/javascript" src="_static/underscore.js"></script>
+ <script type="text/javascript" src="_static/doctools.js"></script>
+ <script type="text/javascript" src="_static/language_data.js"></script>
+
+ <script type="text/javascript" src="_static/js/theme.js"></script>
-
+
+
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
-
-
- <script src="_static/js/modernizr.min.js"></script>
-
</head>
<body class="wy-body-for-nav">
<div class="wy-grid-for-nav">
-
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
<div class="wy-side-scroll">
- <div class="wy-side-nav-search">
+ <div class="wy-side-nav-search" >
@@ -166,41 +168,41 @@ heterogeneous GWAS summary statistics and performs standardization and quality c
<h1>Overview<a class="headerlink" href="#overview" title="Permalink to this headline">¶</a></h1>
<p>The QC and preprocessing step goes as follow:</p>
<ul class="simple">
-<li>map column from of a specific GWAS to standardize names</li>
-<li>Select GWAS SNPs that are in the input reference panel</li>
-<li>Align coded allele of the GWAS with the reference panel</li>
-<li>Infer Number of sample by SNPs if not present in input data</li>
-<li>Filter SNPs with a small sample size</li>
-<li>Normalize the effect size by sample size to have Z-scores</li>
-<li>Save the output by chromosome as the following example:</li>
+<li><p>map column from of a specific GWAS to standardize names</p></li>
+<li><p>Select GWAS SNPs that are in the input reference panel</p></li>
+<li><p>Align coded allele of the GWAS with the reference panel</p></li>
+<li><p>Infer Number of sample by SNPs if not present in input data</p></li>
+<li><p>Filter SNPs with a small sample size</p></li>
+<li><p>Normalize the effect size by sample size to have Z-scores</p></li>
+<li><p>Save the output by chromosome as the following example:</p></li>
</ul>
-<table border="1" class="docutils">
+<table class="docutils align-default">
<colgroup>
-<col width="28%" />
-<col width="19%" />
-<col width="17%" />
-<col width="14%" />
-<col width="22%" />
+<col style="width: 28%" />
+<col style="width: 19%" />
+<col style="width: 17%" />
+<col style="width: 14%" />
+<col style="width: 22%" />
</colgroup>
-<thead valign="bottom">
-<tr class="row-odd"><th class="head">rsID</th>
-<th class="head">pos</th>
-<th class="head">A0</th>
-<th class="head">A1</th>
-<th class="head">Z</th>
+<thead>
+<tr class="row-odd"><th class="head"><p>rsID</p></th>
+<th class="head"><p>pos</p></th>
+<th class="head"><p>A0</p></th>
+<th class="head"><p>A1</p></th>
+<th class="head"><p>Z</p></th>
</tr>
</thead>
-<tbody valign="top">
-<tr class="row-even"><td>rs6548219</td>
-<td>30762</td>
-<td>A</td>
-<td>G</td>
-<td>-1.133</td>
+<tbody>
+<tr class="row-even"><td><p>rs6548219</p></td>
+<td><p>30762</p></td>
+<td><p>A</p></td>
+<td><p>G</p></td>
+<td><p>-1.133</p></td>
</tr>
</tbody>
</table>
<ul class="simple">
-<li>(Optional) Save the output to one file with a chromosome column</li>
+<li><p>(Optional) Save the output to one file with a chromosome column</p></li>
</ul>
<p>(input format needed to perform LD-score)</p>
</div>
@@ -214,170 +216,147 @@ heterogeneous GWAS summary statistics and performs standardization and quality c
<div class="section" id="input">
<h1>Input<a class="headerlink" href="#input" title="Permalink to this headline">¶</a></h1>
<ul class="simple">
-<li>A reference panel (1000 genome format). The user is expected to provide a reference panel in tsv format with the following columns in that order, without header:</li>
+<li><p>A reference panel (1000 genome format). The user is expected to provide a reference panel in tsv format with the following columns in that order, without header:</p></li>
</ul>
-<table border="1" class="docutils">
+<table class="docutils align-default">
<colgroup>
-<col width="12%" />
-<col width="12%" />
-<col width="29%" />
-<col width="12%" />
-<col width="12%" />
-<col width="22%" />
+<col style="width: 12%" />
+<col style="width: 12%" />
+<col style="width: 29%" />
+<col style="width: 12%" />
+<col style="width: 12%" />
+<col style="width: 22%" />
</colgroup>
-<thead valign="bottom">
-<tr class="row-odd"><th class="head">chr</th>
-<th class="head">pos</th>
-<th class="head">snp_id</th>
-<th class="head">ref</th>
-<th class="head">alt</th>
-<th class="head">MAF</th>
+<thead>
+<tr class="row-odd"><th class="head"><p>chr</p></th>
+<th class="head"><p>pos</p></th>
+<th class="head"><p>snp_id</p></th>
+<th class="head"><p>ref</p></th>
+<th class="head"><p>alt</p></th>
+<th class="head"><p>MAF</p></th>
</tr>
</thead>
-<tbody valign="top">
-<tr class="row-even"><td>1</td>
-<td>13116</td>
-<td>rs62635286</td>
-<td>T</td>
-<td>G</td>
-<td>0.0970447</td>
+<tbody>
+<tr class="row-even"><td><p>1</p></td>
+<td><p>13116</p></td>
+<td><p>rs62635286</p></td>
+<td><p>T</p></td>
+<td><p>G</p></td>
+<td><p>0.0970447</p></td>
</tr>
-<tr class="row-odd"><td>1</td>
-<td>13118</td>
-<td>rs200579949</td>
-<td>A</td>
-<td>G</td>
-<td>0.0970447</td>
+<tr class="row-odd"><td><p>1</p></td>
+<td><p>13118</p></td>
+<td><p>rs200579949</p></td>
+<td><p>A</p></td>
+<td><p>G</p></td>
+<td><p>0.0970447</p></td>
</tr>
-<tr class="row-even"><td>1</td>
-<td>14604</td>
-<td>rs541940975</td>
-<td>A</td>
-<td>G</td>
-<td>0.147564</td>
+<tr class="row-even"><td><p>1</p></td>
+<td><p>14604</p></td>
+<td><p>rs541940975</p></td>
+<td><p>A</p></td>
+<td><p>G</p></td>
+<td><p>0.147564</p></td>
</tr>
-<tr class="row-odd"><td>1</td>
-<td>14930</td>
-<td>rs75454623</td>
-<td>A</td>
-<td>G</td>
-<td>0.482228</td>
+<tr class="row-odd"><td><p>1</p></td>
+<td><p>14930</p></td>
+<td><p>rs75454623</p></td>
+<td><p>A</p></td>
+<td><p>G</p></td>
+<td><p>0.482228</p></td>
</tr>
</tbody>
</table>
<ul class="simple">
-<li>Folder containing all raw gwas data (all chromosomes in one file) (minimal conditions?? tab separated?)</li>
-<li>a list containing the name of GWAS file to the string format.</li>
-<li>A descriptor csv files that will described each GWAS summary statistic files:<ul>
-<li>a header</li>
-<li>1 line per study</li>
-<li>the fields are:</li>
+<li><p>Folder containing all raw gwas data : (all chromosomes in one file) (minimal conditions?? tab separated?)</p></li>
+<li><p>a list containing the name of GWAS file to the string format.</p></li>
+<li><p>A descriptor csv files that will described each GWAS summary statistic files:</p>
+<ul>
+<li><p>a header</p></li>
+<li><p>1 line per study</p></li>
+<li><p>the fields are:</p></li>
</ul>
</li>
</ul>
-<table border="1" class="docutils">
-<colgroup>
-<col width="42%" />
-<col width="58%" />
-</colgroup>
-<thead valign="bottom">
-<tr class="row-odd"><th class="head">category</th>
-<th class="head">field name</th>
-</tr>
-</thead>
-<tbody valign="top">
-<tr class="row-even"><td>path to the data</td>
-<td>filename</td>
-</tr>
-<tr class="row-odd"><td>study info fields</td>
-<td>consortia,outcome,fullName,type,Nsample,Ncase,Ncontrol,Nsnp</td>
-</tr>
-<tr class="row-even"><td>names of the header in the GWAS file</td>
-<td>snpid,a1,a2,freq,pval,n,z,OR,se,code,imp,ncas,ncont</td>
-</tr>
-</tbody>
-</table>
+<p>Note that the combination of Consortium and outcome must be unique because it will be used as an index in the cleaning process.</p>
<p>Here is an example of descriptor field, the field irrelevant (for example odd ratio for continuous trait) for the study must be filled with na.</p>
-<table border="1" class="docutils" id="id1">
+<table class="docutils align-default" id="id1">
<caption><span class="caption-text">GWAS information table!</span><a class="headerlink" href="#id1" title="Permalink to this table">¶</a></caption>
<colgroup>
-<col width="5%" />
-<col width="5%" />
-<col width="5%" />
-<col width="5%" />
-<col width="5%" />
-<col width="5%" />
-<col width="5%" />
-<col width="5%" />
-<col width="5%" />
-<col width="5%" />
-<col width="5%" />
-<col width="5%" />
-<col width="5%" />
-<col width="5%" />
-<col width="5%" />
-<col width="5%" />
-<col width="5%" />
-<col width="5%" />
-<col width="5%" />
-<col width="5%" />
-<col width="5%" />
-<col width="5%" />
+<col style="width: 5%" />
+<col style="width: 5%" />
+<col style="width: 5%" />
+<col style="width: 5%" />
+<col style="width: 5%" />
+<col style="width: 5%" />
+<col style="width: 5%" />
+<col style="width: 5%" />
+<col style="width: 5%" />
+<col style="width: 5%" />
+<col style="width: 5%" />
+<col style="width: 5%" />
+<col style="width: 5%" />
+<col style="width: 5%" />
+<col style="width: 5%" />
+<col style="width: 5%" />
+<col style="width: 5%" />
+<col style="width: 5%" />
+<col style="width: 5%" />
+<col style="width: 5%" />
+<col style="width: 5%" />
+<col style="width: 5%" />
</colgroup>
-<tbody valign="top">
-<tr class="row-odd"><td><table class="first last 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">header:</th><td class="field-body">“filenameâ€</td>
-</tr>
-</tbody>
-</table>
+<tbody>
+<tr class="row-odd"><td><dl class="field-list simple">
+<dt class="field-odd">header</dt>
+<dd class="field-odd"><p>“filenameâ€</p>
+</dd>
+</dl>
</td>
-<td>consortia</td>
-<td>outcome</td>
-<td>fullName</td>
-<td>type</td>
-<td>Nsample</td>
-<td>Ncase</td>
-<td>Ncontrol</td>
-<td>Nsnp</td>
-<td>snpid</td>
-<td>a1</td>
-<td>a2</td>
-<td>freq</td>
-<td>pval</td>
-<td>n</td>
-<td>z</td>
-<td>OR</td>
-<td>se</td>
-<td>code</td>
-<td>imp</td>
-<td>ncas</td>
-<td>ncont</td>
+<td><p>consortia</p></td>
+<td><p>outcome</p></td>
+<td><p>fullName</p></td>
+<td><p>type</p></td>
+<td><p>Nsample</p></td>
+<td><p>Ncase</p></td>
+<td><p>Ncontrol</p></td>
+<td><p>Nsnp</p></td>
+<td><p>snpid</p></td>
+<td><p>a1</p></td>
+<td><p>a2</p></td>
+<td><p>freq</p></td>
+<td><p>pval</p></td>
+<td><p>n</p></td>
+<td><p>z</p></td>
+<td><p>OR</p></td>
+<td><p>se</p></td>
+<td><p>code</p></td>
+<td><p>imp</p></td>
+<td><p>ncas</p></td>
+<td><p>ncont</p></td>
</tr>
-<tr class="row-even"><td>GIANT_HEIGHT_Wood_et_al.txt</td>
-<td>GIANT</td>
-<td>HEIGHT</td>
-<td>Height</td>
-<td>Anthropometry</td>
-<td>253288</td>
-<td>na</td>
-<td>na</td>
-<td>2550858</td>
-<td>MarkerName</td>
-<td>Allele1</td>
-<td>Allele2</td>
-<td>Freq.Allele1.HapMapCEU</td>
-<td>p</td>
-<td>N</td>
-<td>b</td>
-<td>na</td>
-<td>SE</td>
-<td>na</td>
-<td>na</td>
-<td>na</td>
-<td>na</td>
+<tr class="row-even"><td><p>GIANT_HEIGHT_Wood_et_al.txt</p></td>
+<td><p>GIANT</p></td>
+<td><p>HEIGHT</p></td>
+<td><p>Height</p></td>
+<td><p>Anthropometry</p></td>
+<td><p>253288</p></td>
+<td><p>na</p></td>
+<td><p>na</p></td>
+<td><p>2550858</p></td>
+<td><p>MarkerName</p></td>
+<td><p>Allele1</p></td>
+<td><p>Allele2</p></td>
+<td><p>Freq.Allele1.HapMapCEU</p></td>
+<td><p>p</p></td>
+<td><p>N</p></td>
+<td><p>b</p></td>
+<td><p>na</p></td>
+<td><p>SE</p></td>
+<td><p>na</p></td>
+<td><p>na</p></td>
+<td><p>na</p></td>
+<td><p>na</p></td>
</tr>
</tbody>
</table>
@@ -385,74 +364,62 @@ heterogeneous GWAS summary statistics and performs standardization and quality c
<div class="section" id="command-line-usage-example">
<h1>Command line usage example:<a class="headerlink" href="#command-line-usage-example" title="Permalink to this headline">¶</a></h1>
<p>It is possible to launch the complete preprocessing (all steps described in section Overview section) from the command line:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">usage</span><span class="p">:</span> <span class="n">jass_preprocessing</span> <span class="p">[</span><span class="o">-</span><span class="n">h</span><span class="p">]</span> <span class="o">--</span><span class="n">percent</span><span class="o">-</span><span class="n">sample</span><span class="o">-</span><span class="n">size</span> <span class="n">PERCENT_SAMPLE_SIZE</span>
- <span class="o">--</span><span class="n">gwas</span><span class="o">-</span><span class="n">info</span> <span class="n">GWAS_INFO</span> <span class="o">--</span><span class="n">ref</span><span class="o">-</span><span class="n">folder</span> <span class="n">REF_FOLDER</span>
- <span class="o">--</span><span class="n">gwas</span><span class="o">-</span><span class="n">folder</span> <span class="n">GWAS_FOLDER</span> <span class="o">--</span><span class="n">output</span><span class="o">-</span><span class="n">folder</span>
- <span class="n">OUTPUT_FOLDER</span>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">usage</span><span class="p">:</span> <span class="n">jass_preprocessing</span> <span class="p">[</span><span class="o">-</span><span class="n">h</span><span class="p">]</span> <span class="o">--</span><span class="n">gwas</span><span class="o">-</span><span class="n">info</span> <span class="n">GWAS_INFO</span> <span class="o">--</span><span class="n">ref</span><span class="o">-</span><span class="n">path</span> <span class="n">REF_PATH</span>
+ <span class="o">--</span><span class="nb">input</span><span class="o">-</span><span class="n">folder</span> <span class="n">INPUT_FOLDER</span> <span class="o">--</span><span class="n">diagnostic</span><span class="o">-</span><span class="n">folder</span>
+ <span class="n">DIAGNOSTIC_FOLDER</span> <span class="o">--</span><span class="n">output</span><span class="o">-</span><span class="n">folder</span> <span class="n">OUTPUT_FOLDER</span>
<span class="p">[</span><span class="o">--</span><span class="n">output</span><span class="o">-</span><span class="n">folder</span><span class="o">-</span><span class="mi">1</span><span class="o">-</span><span class="n">file</span> <span class="n">OUTPUT_FOLDER_1_FILE</span><span class="p">]</span>
+ <span class="p">[</span><span class="o">--</span><span class="n">percent</span><span class="o">-</span><span class="n">sample</span><span class="o">-</span><span class="n">size</span> <span class="n">PERCENT_SAMPLE_SIZE</span><span class="p">]</span>
+ <span class="p">[</span><span class="o">--</span><span class="n">minimum</span><span class="o">-</span><span class="n">MAF</span> <span class="n">MINIMUM_MAF</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">mask</span><span class="o">-</span><span class="n">MHC</span> <span class="n">MASK_MHC</span><span class="p">]</span>
+ <span class="p">[</span><span class="o">--</span><span class="n">additional</span><span class="o">-</span><span class="n">masked</span><span class="o">-</span><span class="n">region</span> <span class="n">ADDITIONAL_MASKED_REGION</span><span class="p">]</span>
</pre></div>
</div>
<div class="section" id="Named Arguments">
<h2>Named Arguments<a class="headerlink" href="#Named Arguments" title="Permalink to this headline">¶</a></h2>
-<table class="docutils option-list" frame="void" rules="none">
-<col class="option" />
-<col class="description" />
-<tbody valign="top">
-<tr><td class="option-group" colspan="2">
-<kbd>--percent-sample-size</kbd></td>
-</tr>
-<tr><td> </td><td>the proportion of the 90th percentile of the sample size used to filter the SNPs</td></tr>
-<tr><td class="option-group">
-<kbd>--gwas-info</kbd></td>
-<td>Path to the file describing the format of the individual GWASs files</td></tr>
-<tr><td class="option-group">
-<kbd>--ref-folder</kbd></td>
-<td>reference panel location (used to determine which snp to impute)</td></tr>
-<tr><td class="option-group">
-<kbd>--gwas-folder</kbd></td>
-<td><blockquote class="first last">
-<div>Path to the folder containing the GWASs summ stat files, must end by ‘/’</div></blockquote>
-</td></tr>
-<tr><td class="option-group" colspan="2">
-<kbd>--output-folder</kbd></td>
-</tr>
-<tr><td> </td><td>Location of main ouput folder for preprocessed GWAS files (splitted by chromosome)</td></tr>
-<tr><td class="option-group" colspan="2">
-<kbd>--output-folder-1-file</kbd></td>
-</tr>
-<tr><td> </td><td>optional location to store the preprocessing in one tabular file with one chromosome columns</td></tr>
-</tbody>
-</table>
+<dl class="option-list">
+<dt><kbd>--gwas-info</kbd></dt>
+<dd><p>Path to the file describing the format of the individual GWASs files with correct header</p>
+</dd>
+<dt><kbd>--ref-path</kbd></dt>
+<dd><p>reference panel location (used to determine which snp to impute)</p>
+</dd>
+<dt><kbd>--input-folder</kbd></dt>
+<dd><p>Path to the folder containing the Raw GWASs summary statistic files, must end by ‘/’</p>
+</dd>
+<dt><kbd>--diagnostic-folder</kbd></dt>
+<dd><p>Path to the reporting information on the PreProcessing such as the SNPs sample size distribution</p>
+</dd>
+<dt><kbd>--output-folder</kbd></dt>
+<dd><p>Location of main ouput folder for preprocessed GWAS files (splitted by chromosome)</p>
+</dd>
+<dt><kbd>--output-folder-1-file</kbd></dt>
+<dd><p>optional location to store the preprocessing in one tabular file with one chromosome columns (useful to compute LDSC correlation for instance)</p>
+</dd>
+<dt><kbd>--percent-sample-size</kbd></dt>
+<dd><p>the proportion (between 0 and 1) of the 90th percentile of the sample size used to filter the SNPs</p>
+<p>Default: 0.7</p>
+</dd>
+<dt><kbd>--minimum-MAF</kbd></dt>
+<dd><p>Filter the reference panel by minimum allele frequency</p>
+<p>Default: 0.01</p>
+</dd>
+<dt><kbd>--mask-MHC</kbd></dt>
+<dd><p>Whether the MHC region should be masked or not. default is False</p>
+<p>Default: False</p>
+</dd>
+<dt><kbd>--additional-masked-region</kbd></dt>
+<dd><p>List of dictionary containing coordinate of region to mask. For example :[{‘chr’:6, ‘start’:50000000, ‘end’: 70000000}, {‘chr’:6, ‘start’:100000000, ‘end’: 120000000}]</p>
+</dd>
+</dl>
</div>
</div>
<div class="section" id="indices-and-tables">
<h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this headline">¶</a></h1>
<ul class="simple">
-<li><a class="reference internal" href="genindex.html"><span class="std std-ref">Index</span></a></li>
-<li><a class="reference internal" href="py-modindex.html"><span class="std std-ref">Module Index</span></a></li>
+<li><p><a class="reference internal" href="genindex.html"><span class="std std-ref">Index</span></a></p></li>
+<li><p><a class="reference internal" href="py-modindex.html"><span class="std std-ref">Module Index</span></a></p></li>
</ul>
-<span class="target" id="module-impute_jass"></span><table border="1" class="longtable docutils">
-<colgroup>
-<col width="10%" />
-<col width="90%" />
-</colgroup>
-<tbody valign="top">
-<tr class="row-odd"><td><code class="xref py py-obj docutils literal notranslate"><span class="pre">imputation_launcher</span></code></td>
-<td>Imputation launcher</td>
-</tr>
-<tr class="row-even"><td><code class="xref py py-obj docutils literal notranslate"><span class="pre">ld_matrix</span></code></td>
-<td>Function set to compute LD correlation from a reference panel in predefined Region</td>
-</tr>
-<tr class="row-odd"><td><code class="xref py py-obj docutils literal notranslate"><span class="pre">stat_models</span></code></td>
-<td>This module contain the statistical library for imputation.</td>
-</tr>
-<tr class="row-even"><td><code class="xref py py-obj docutils literal notranslate"><span class="pre">windows</span></code></td>
-<td>implement the imputation window is sliding along the genome:</td>
-</tr>
-</tbody>
-</table>
<ul class="simple">
-<li><a class="reference internal" href="search.html"><span class="std std-ref">Search Page</span></a></li>
+<li><p><a class="reference internal" href="search.html"><span class="std std-ref">Search Page</span></a></p></li>
</ul>
</div>
@@ -484,25 +451,16 @@ heterogeneous GWAS summary statistics and performs standardization and quality c
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+ </script>
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diff --git a/doc/_build/html/objects.inv b/doc/_build/html/objects.inv
index f516960de89418426bd3e9053677ae0cb36091f7..82a46b99e139cbf660b44a2c0de0fb5639805a65 100644
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diff --git a/doc/_build/html/py-modindex.html b/doc/_build/html/py-modindex.html
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--- a/doc/_build/html/py-modindex.html
+++ b/doc/_build/html/py-modindex.html
@@ -17,13 +17,20 @@
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-
+ <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>
+ <script type="text/javascript" src="_static/jquery.js"></script>
+ <script type="text/javascript" src="_static/underscore.js"></script>
+ <script type="text/javascript" src="_static/doctools.js"></script>
+ <script type="text/javascript" src="_static/language_data.js"></script>
+
+ <script type="text/javascript" src="_static/js/theme.js"></script>
-
+
+
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<link rel="index" title="Index" href="genindex.html" />
@@ -31,21 +38,16 @@
-
-
- <script src="_static/js/modernizr.min.js"></script>
-
</head>
<body class="wy-body-for-nav">
<div class="wy-grid-for-nav">
-
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<div class="wy-side-scroll">
- <div class="wy-side-nav-search">
+ <div class="wy-side-nav-search" >
@@ -143,27 +145,18 @@
<h1>Python Module Index</h1>
<div class="modindex-jumpbox">
- <a href="#cap-i"><strong>i</strong></a> |
<a href="#cap-j"><strong>j</strong></a>
</div>
<table class="indextable modindextable">
<tr class="pcap"><td></td><td> </td><td></td></tr>
- <tr class="cap" id="cap-i"><td></td><td>
- <strong>i</strong></td><td></td></tr>
- <tr>
- <td></td>
- <td>
- <a href="index.html#module-impute_jass"><code class="xref">impute_jass</code></a></td><td>
- <em></em></td></tr>
- <tr class="pcap"><td></td><td> </td><td></td></tr>
<tr class="cap" id="cap-j"><td></td><td>
<strong>j</strong></td><td></td></tr>
<tr>
<td><img src="_static/minus.png" class="toggler"
id="toggle-1" style="display: none" alt="-" /></td>
<td>
- <code class="xref">jass_preprocessing</code></td><td>
+ <a href="_autosummary/jass_preprocessing.html#module-jass_preprocessing"><code class="xref">jass_preprocessing</code></a></td><td>
<em></em></td></tr>
<tr class="cg-1">
<td></td>
@@ -220,25 +213,16 @@
-
-
-
-
- <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
- <script type="text/javascript" src="_static/jquery.js"></script>
- <script type="text/javascript" src="_static/underscore.js"></script>
- <script type="text/javascript" src="_static/doctools.js"></script>
-
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-
<script type="text/javascript">
jQuery(function () {
SphinxRtdTheme.Navigation.enable(true);
});
- </script>
+ </script>
+
+
+
+
+
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</html>
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diff --git a/doc/_build/html/search.html b/doc/_build/html/search.html
index 62ecb37628ef420deec8f8d1e5a53b1a5282468c..b5326cce8c011ad4870a333844a3d1b3995a2fb6 100644
--- a/doc/_build/html/search.html
+++ b/doc/_build/html/search.html
@@ -17,32 +17,35 @@
-
-
+ <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>
+ <script type="text/javascript" src="_static/jquery.js"></script>
+ <script type="text/javascript" src="_static/underscore.js"></script>
+ <script type="text/javascript" src="_static/doctools.js"></script>
+ <script type="text/javascript" src="_static/language_data.js"></script>
+ <script type="text/javascript" src="_static/searchtools.js"></script>
+
+ <script type="text/javascript" src="_static/js/theme.js"></script>
-
+
+
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="#" />
-
-
- <script src="_static/js/modernizr.min.js"></script>
-
</head>
<body class="wy-body-for-nav">
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-
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<div class="wy-side-scroll">
- <div class="wy-side-nav-search">
+ <div class="wy-side-nav-search" >
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-
<script type="text/javascript">
jQuery(function () {
SphinxRtdTheme.Navigation.enable(true);
});
</script>
+
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+
+
+
<script type="text/javascript">
jQuery(function() { Search.loadIndex("searchindex.js"); });
</script>
diff --git a/doc/_build/html/searchindex.js b/doc/_build/html/searchindex.js
index 93bbf73e7025bebc49b6198c0ad38be9fbd45c86..aeb01f725fe7101101e31f11be38f6557eefe2d8 100644
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diff --git a/doc/source/reference.bib b/doc/source/reference.bib
new file mode 100644
index 0000000000000000000000000000000000000000..83b447b068cdad124a11dcb33d854b95420da7db
--- /dev/null
+++ b/doc/source/reference.bib
@@ -0,0 +1,48 @@
+@article{Pasaniuc2014,
+abstract = {MOTIVATION Imputation using external reference panels (e.g. 1000 Genomes) is a widely used approach for increasing power in genome-wide association studies and meta-analysis. Existing hidden Markov models (HMM)-based imputation approaches require individual-level genotypes. Here, we develop a new method for Gaussian imputation from summary association statistics, a type of data that is becoming widely available. RESULTS In simulations using 1000 Genomes (1000G) data, this method recovers 84{\%} (54{\%}) of the effective sample size for common ({\textgreater}5{\%}) and low-frequency (1-5{\%}) variants [increasing to 87{\%} (60{\%}) when summary linkage disequilibrium information is available from target samples] versus the gold standard of 89{\%} (67{\%}) for HMM-based imputation, which cannot be applied to summary statistics. Our approach accounts for the limited sample size of the reference panel, a crucial step to eliminate false-positive associations, and it is computationally very fast. As an empirical demonstration, we apply our method to seven case-control phenotypes from the Wellcome Trust Case Control Consortium (WTCCC) data and a study of height in the British 1958 birth cohort (1958BC). Gaussian imputation from summary statistics recovers 95{\%} (105{\%}) of the effective sample size (as quantified by the ratio of [Formula: see text] association statistics) compared with HMM-based imputation from individual-level genotypes at the 227 (176) published single nucleotide polymorphisms (SNPs) in the WTCCC (1958BC height) data. In addition, for publicly available summary statistics from large meta-analyses of four lipid traits, we publicly release imputed summary statistics at 1000G SNPs, which could not have been obtained using previously published methods, and demonstrate their accuracy by masking subsets of the data. We show that 1000G imputation using our approach increases the magnitude and statistical evidence of enrichment at genic versus non-genic loci for these traits, as compared with an analysis without 1000G imputation. Thus, imputation of summary statistics will be a valuable tool in future functional enrichment analyses. AVAILABILITY AND IMPLEMENTATION Publicly available software package available at http://bogdan.bioinformatics.ucla.edu/software/. CONTACT bpasaniuc@mednet.ucla.edu or aprice@hsph.harvard.edu SUPPLEMENTARY INFORMATION Supplementary materials are available at Bioinformatics online.},
+archivePrefix = {arXiv},
+arxivId = {arXiv:1309.3258v1},
+author = {Pasaniuc, Bogdan and Zaitlen, Noah and Shi, Huwenbo and Bhatia, Gaurav and Gusev, Alexander and Pickrell, Joseph and Hirschhorn, Joel and Strachan, David P. and Patterson, Nick and Price, Alkes L.},
+doi = {10.1093/bioinformatics/btu416},
+eprint = {arXiv:1309.3258v1},
+file = {:home/hjulienn/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Pasaniuc et al. - 2014 - Fast and accurate imputation of summary statistics enhances evidence of functional enrichment.pdf:pdf},
+issn = {13674811},
+journal = {Bioinformatics (Oxford, England)},
+keywords = {Hughes},
+mendeley-tags = {Hughes},
+number = {20},
+pages = {2906--2914},
+pmid = {24990607},
+title = {{Fast and accurate imputation of summary statistics enhances evidence of functional enrichment}},
+volume = {30},
+year = {2014}
+}
+
+@article{Berisa2015,
+abstract = {We present a method to identify approximately independent blocks of linkage disequilibrium (LD) in the human genome. These blocks enable automated analysis of multiple genome-wide association studies.},
+author = {Berisa, Tomaz and Pickrell, Joseph K.},
+doi = {10.1093/bioinformatics/btv546},
+file = {:home/hjulienn/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Berisa, Pickrell - 2015 - Approximately independent linkage disequilibrium blocks in human populations.pdf:pdf},
+isbn = {1367-4811 (Electronic) 1367-4803 (Linking)},
+issn = {14602059},
+journal = {Bioinformatics},
+mendeley-groups = {Genetics},
+number = {2},
+pages = {283--285},
+pmid = {26395773},
+title = {{Approximately independent linkage disequilibrium blocks in human populations}},
+volume = {32},
+year = {2015}
+}
+
+
+@article{lee2013dist,
+ title={DIST: direct imputation of summary statistics for unmeasured SNPs},
+ author={Lee, Donghyung and Bigdeli, T Bernard and Riley, Brien P and Fanous, Ayman H and Bacanu, Silviu-Alin},
+ journal={Bioinformatics},
+ volume={29},
+ number={22},
+ pages={2925--2927},
+ year={2013},
+ publisher={Oxford University Press}
+}
diff --git a/jass_preprocessing/__main__.py b/jass_preprocessing/__main__.py
index 6c989c09c98812d26452b54f4dc94e5407576fd8..b9ca5f386b3bd6a3288af332e2bf11b3e718d5ef 100644
--- a/jass_preprocessing/__main__.py
+++ b/jass_preprocessing/__main__.py
@@ -48,7 +48,7 @@ def launch_preprocessing(args):
GWAS_link = jp.map_gwas.walkfs(args.input_folder, gwas_filename)[2]
mapgw = jp.map_gwas.map_columns_position(GWAS_link, gwas_map.loc[tag])
- gw_df = jp.map_gwas.read_gwas(GWAS_link, mapgw)
+ gw_df = jp.map_gwas.read_gwas(GWAS_link, mapgw, imputation_treshold=eval(args.imputation_quality_treshold))
if args.additional_masked_region is None:
ref = jp.map_reference.read_reference(args.ref_path, bool(args.mask_MHC), float(args.minimum_MAF))
@@ -85,6 +85,8 @@ def add_preprocessing_argument():
parser.add_argument('--mask-MHC', required=False, help= "Whether the MHC region should be masked or not. default is False", default=False)
parser.add_argument('--additional-masked-region', required=False, help= "List of dictionary containing coordinate of region to mask. For example :[{'chr':6, 'start':50000000, 'end': 70000000}, {'chr':6, 'start':100000000, 'end': 120000000}]", default=None)
+ parser.add_argument('--imputation-quality-treshold', required=False, help= "minimum imputation quality in summary statistics", default=None)
+
parser.set_defaults(func=launch_preprocessing)
return parser
diff --git a/jass_preprocessing/__pycache__/compute_score.cpython-35.pyc b/jass_preprocessing/__pycache__/compute_score.cpython-35.pyc
index b2269fda3bde8364ba13e9146007998e0f9aa6cb..f309bb5578658c372a0bb4aeeb4dcf60206238ee 100644
Binary files a/jass_preprocessing/__pycache__/compute_score.cpython-35.pyc and b/jass_preprocessing/__pycache__/compute_score.cpython-35.pyc differ
diff --git a/jass_preprocessing/__pycache__/map_gwas.cpython-35.pyc b/jass_preprocessing/__pycache__/map_gwas.cpython-35.pyc
index c7ec3b42eabafcaddf309b681081255d9931337e..33f12606fa632933c72b40bde5f16c076d365a8b 100644
Binary files a/jass_preprocessing/__pycache__/map_gwas.cpython-35.pyc and b/jass_preprocessing/__pycache__/map_gwas.cpython-35.pyc differ
diff --git a/jass_preprocessing/__pycache__/map_reference.cpython-35.pyc b/jass_preprocessing/__pycache__/map_reference.cpython-35.pyc
index e0226d72d0a5b90b2e537f6dd35d4fdb9a64b645..d03d20df9c848f4a7b393963c7ac3aa0c54e76a8 100644
Binary files a/jass_preprocessing/__pycache__/map_reference.cpython-35.pyc and b/jass_preprocessing/__pycache__/map_reference.cpython-35.pyc differ
diff --git a/jass_preprocessing/map_gwas.py b/jass_preprocessing/map_gwas.py
index 0f5c35b96720649df8aadb4bd0bc1d4ffa5f220c..19a0d3cfb134718ea92d728bab9feb0367027d7d 100644
--- a/jass_preprocessing/map_gwas.py
+++ b/jass_preprocessing/map_gwas.py
@@ -121,7 +121,7 @@ def map_columns_position(gwas_internal_link, column_dict):
f.close()
return mapgw
-def read_gwas( gwas_internal_link, column_map):
+def read_gwas( gwas_internal_link, column_map, imputation_treshold=None):
"""
Read gwas raw data, fetch columns thanks to position stored in
column_map and rename columns according to column_map.index
@@ -155,6 +155,8 @@ def read_gwas( gwas_internal_link, column_map):
print(fullGWAS.head())
fullGWAS.set_index("snpid", inplace=True)
print(fullGWAS.head())
+ if imputation_treshold:
+ fullGWAS = fullGWAS.loc[fullName.imputation_quality > imputation_treshold]
fullGWAS = fullGWAS[~fullGWAS.index.duplicated(keep='first')]
#fullGWAS = convert_missing_values(fullGWAS)