diff --git a/doc/_build/doctrees/environment.pickle b/doc/_build/doctrees/environment.pickle
index 37ed4b08a279ba895c90c7a1e3e3234dced8b63f..f5c71c806c0033c18802de52f9650f07ccba2a70 100644
Binary files a/doc/_build/doctrees/environment.pickle and b/doc/_build/doctrees/environment.pickle differ
diff --git a/doc/_build/doctrees/index.doctree b/doc/_build/doctrees/index.doctree
index 554b563fc216964e90e38f90aeecec5d7b9e4ca9..6e782da42779c8fdf7cc36eff0048a4115c4ebed 100644
Binary files a/doc/_build/doctrees/index.doctree and b/doc/_build/doctrees/index.doctree differ
diff --git a/doc/_build/html/_sources/index.rst.txt b/doc/_build/html/_sources/index.rst.txt
index 7136a4067686fa41a885c328bacf6133ea3bde08..733fd0b36cef188589dd8826d06ac14a421f42ea 100644
--- a/doc/_build/html/_sources/index.rst.txt
+++ b/doc/_build/html/_sources/index.rst.txt
@@ -34,18 +34,25 @@ The QC and preprocessing step goes as follow:
| rs6548219| 30762 | A | G | -1.133 |
+----------+-------+------+-----+--------+
+* (Optional) Save the output to one file with a chromosome column
+(input format needed to perform LD-score)
+
++-------+-----------+--------+----+----+-----+-----+
+| chrom | rsID | pos | A0 | A1 | Z | P |
++-------+-----------+--------+----+----+-----+-----+
+| 1 | rs4075116 |1003629 | C | T |0.30 | 0.76|
++-------+-----------+--------+----+----+-----+-----+
+
+
Installation
============
-In a folder that will contain the jass_preprocessing repository,
-execute the following lines:
+In a terminal, execute the following lines:
.. code-block:: shell
pip3 install git+https://gitlab.pasteur.fr/statistical-genetics/JASS_Pre-processing
-
-
Input
======
@@ -86,19 +93,22 @@ Input
.. | I don't know | altNcas,altNcont|
-* it must contain the following columns:
+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.
-Hard coded path (l.20-29 of JASS_Pre-processing/main_preprocessing.py)
+.. csv-table:: GWAS information table!
+ :header: "filename","consortia","outcome","fullName","type","Nsample","Ncase","Ncontrol","Nsnp","snpid","a1","a2","freq","pval","n","z","OR","se","code","imp","ncas","ncont"
+ "GIANT_HEIGHT_Wood_et_al.txt","GIANT","HEIGHT","Height","Anthropometry",253288, na, na, 2550858, "MarkerName", "Allele1", "Allele2", "Freq.Allele1.HapMapCEU","p","N","b",na,"SE",na,na,na,na
Command line usage example:
============================
-It is possible to launch the complete preprocessing from the command line:
+It is possible to launch the complete preprocessing (all steps described in section Overview section) from the command line:
.. argparse::
:ref: jass_preprocessing.__main__.add_preprocessing_argument
+ :prog: jass_preprocessing
Indices and tables
==================
@@ -106,4 +116,6 @@ Indices and tables
* :ref:`genindex`
* :ref:`modindex`
+.. automodule:: impute_jass
+ :members:
* :ref:`search`
diff --git a/doc/_build/html/genindex.html b/doc/_build/html/genindex.html
index d087160a11e743638e35b4cd4154d466406ea6ad..aa1da30101863920b3e9f57a1df961575fdf94dd 100644
--- a/doc/_build/html/genindex.html
+++ b/doc/_build/html/genindex.html
@@ -146,6 +146,7 @@
<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>
@@ -193,6 +194,14 @@
</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>
diff --git a/doc/_build/html/index.html b/doc/_build/html/index.html
index 21c0c2c01a732fe52a7ac3417783ddae791546a8..d124afb3069da18a5b06ba4684faa0fc958012f2 100644
--- a/doc/_build/html/index.html
+++ b/doc/_build/html/index.html
@@ -199,11 +199,14 @@ heterogeneous GWAS summary statistics and performs standardization and quality c
</tr>
</tbody>
</table>
+<ul class="simple">
+<li>(Optional) Save the output to one file with a chromosome column</li>
+</ul>
+<p>(input format needed to perform LD-score)</p>
</div>
<div class="section" id="installation">
<h1>Installation<a class="headerlink" href="#installation" title="Permalink to this headline">¶</a></h1>
-<p>In a folder that will contain the jass_preprocessing repository,
-execute the following lines:</p>
+<p>In a terminal, execute the following lines:</p>
<div class="highlight-shell notranslate"><div class="highlight"><pre><span></span>pip3 install git+https://gitlab.pasteur.fr/statistical-genetics/JASS_Pre-processing
</pre></div>
</div>
@@ -294,18 +297,99 @@ execute the following lines:</p>
</tr>
</tbody>
</table>
-<ul class="simple">
-<li>it must contain the following columns:</li>
-</ul>
-<p>Hard coded path (l.20-29 of JASS_Pre-processing/main_preprocessing.py)</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">
+<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%" />
+</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>
+</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>
+</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>
+</tbody>
+</table>
</div>
<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 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">sphinx</span><span class="o">-</span><span class="n">build</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>
- <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>
+<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>
+ <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>
</pre></div>
</div>
<div class="section" id="Named Arguments">
@@ -346,6 +430,28 @@ execute the following lines:</p>
<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>
+</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>
</ul>
</div>
diff --git a/doc/_build/html/objects.inv b/doc/_build/html/objects.inv
index 744ac39d6336c598784b1426b95e4a81055a31b5..f516960de89418426bd3e9053677ae0cb36091f7 100644
Binary files a/doc/_build/html/objects.inv and b/doc/_build/html/objects.inv differ
diff --git a/doc/_build/html/py-modindex.html b/doc/_build/html/py-modindex.html
index 0bf1ea8b0ce87de824984e3a2ec94e25292d287b..06b433b7bc569719755d71b88cfe650831337ef2 100644
--- a/doc/_build/html/py-modindex.html
+++ b/doc/_build/html/py-modindex.html
@@ -143,11 +143,20 @@
<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>
diff --git a/doc/_build/html/searchindex.js b/doc/_build/html/searchindex.js
index fdd4b2fa7baa3078acee4e7ffe6ccf1dba1b737e..93bbf73e7025bebc49b6198c0ad38be9fbd45c86 100644
--- a/doc/_build/html/searchindex.js
+++ b/doc/_build/html/searchindex.js
@@ -1 +1 @@
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diff --git a/doc/source/index.rst b/doc/source/index.rst
index 8a554cc7528d0462e33804feee04116856cd27b0..733fd0b36cef188589dd8826d06ac14a421f42ea 100644
--- a/doc/source/index.rst
+++ b/doc/source/index.rst
@@ -34,18 +34,25 @@ The QC and preprocessing step goes as follow:
| rs6548219| 30762 | A | G | -1.133 |
+----------+-------+------+-----+--------+
+* (Optional) Save the output to one file with a chromosome column
+(input format needed to perform LD-score)
+
++-------+-----------+--------+----+----+-----+-----+
+| chrom | rsID | pos | A0 | A1 | Z | P |
++-------+-----------+--------+----+----+-----+-----+
+| 1 | rs4075116 |1003629 | C | T |0.30 | 0.76|
++-------+-----------+--------+----+----+-----+-----+
+
+
Installation
============
-In a folder that will contain the jass_preprocessing repository,
-execute the following lines:
+In a terminal, execute the following lines:
.. code-block:: shell
pip3 install git+https://gitlab.pasteur.fr/statistical-genetics/JASS_Pre-processing
-
-
Input
======
@@ -86,10 +93,12 @@ Input
.. | I don't know | altNcas,altNcont|
-* it must contain the following columns:
+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.
-Hard coded path (l.20-29 of JASS_Pre-processing/main_preprocessing.py)
+.. csv-table:: GWAS information table!
+ :header: "filename","consortia","outcome","fullName","type","Nsample","Ncase","Ncontrol","Nsnp","snpid","a1","a2","freq","pval","n","z","OR","se","code","imp","ncas","ncont"
+ "GIANT_HEIGHT_Wood_et_al.txt","GIANT","HEIGHT","Height","Anthropometry",253288, na, na, 2550858, "MarkerName", "Allele1", "Allele2", "Freq.Allele1.HapMapCEU","p","N","b",na,"SE",na,na,na,na
Command line usage example:
@@ -99,6 +108,7 @@ It is possible to launch the complete preprocessing (all steps described in sect
.. argparse::
:ref: jass_preprocessing.__main__.add_preprocessing_argument
+ :prog: jass_preprocessing
Indices and tables
==================