Commit 92a461de authored by hjulienne's avatar hjulienne

add filter imputation quality

parent 8f85b369
Pipeline #19045 passed with stages
in 57 seconds
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......@@ -17,32 +17,34 @@
<script type="text/javascript" src="../_static/js/modernizr.min.js"></script>
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......@@ -154,9 +156,7 @@
<li class="toctree-l2"><a class="reference internal" href="jass_preprocessing.html#module-jass_preprocessing.map_gwas">jass_preprocessing.map_gwas module</a></li>
<li class="toctree-l2"><a class="reference internal" href="jass_preprocessing.html#module-jass_preprocessing.map_reference">jass_preprocessing.map_reference module</a></li>
<li class="toctree-l2"><a class="reference internal" href="jass_preprocessing.html#module-jass_preprocessing.save_output">jass_preprocessing.save_output module</a></li>
<li class="toctree-l2"><a class="reference internal" href="jass_preprocessing.html#module-jass_preprocessing">Module contents</a><ul class="simple">
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="jass_preprocessing.html#module-jass_preprocessing">Module contents</a></li>
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......@@ -191,25 +191,16 @@
<script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
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......@@ -17,32 +17,34 @@
<script type="text/javascript" src="../_static/js/modernizr.min.js"></script>
<script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
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......@@ -171,25 +173,16 @@
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......@@ -17,32 +17,34 @@
<script type="text/javascript" src="../../_static/js/modernizr.min.js"></script>
<script type="text/javascript" id="documentation_options" data-url_root="../../" src="../../_static/documentation_options.js"></script>
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......@@ -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">&quot;&quot;&quot;</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">&#39;n&#39;</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">&quot;Some snp had an infinite sample size&quot;</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">&quot;computed_N&quot;</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>
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......@@ -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>
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......@@ -183,25 +185,16 @@
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<script type="text/javascript" src="../../_static/jquery.js"></script>
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......@@ -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>
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......@@ -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">&quot;&quot;&quot;</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"> &quot;&quot;&quot;</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">&quot;</span><span class="se">\t</span><span class="s2">&quot;</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">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">,</span>
<span class="n">names</span> <span class="o">=</span><span class="p">[</span><span class="s1">&#39;chr&#39;</span><span class="p">,</span> <span class="s2">&quot;pos&quot;</span><span class="p">,</span> <span class="s2">&quot;snp_id&quot;</span><span class="p">,</span> <span class="s2">&quot;ref&quot;</span><span class="p">,</span> <span class="s2">&quot;alt&quot;</span><span class="p">,</span> <span class="s2">&quot;MAF&quot;</span><span class="p">],</span>
<span class="n">index_col</span><span class="o">=</span><span class="s2">&quot;snp_id&quot;</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">&quot;AT&quot;</span><span class="p">,</span> <span class="s2">&quot;TA&quot;</span><span class="p">,</span> <span class="s1">&#39;CG&#39;</span><span class="p">,</span><span class="s1">&#39;GC&#39;</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">&lt;</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">&gt;</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">&gt;</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">&quot;chr&quot;</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">&lt;</span><span class="n">reg</span><span class="p">[</span><span class="s2">&quot;start&quot;</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">&gt;</span> <span class="n">reg</span><span class="p">[</span><span class="s2">&quot;end&quot;</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">&quot;&quot;&quot;</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>
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......@@ -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>
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......@@ -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>
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......@@ -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.
......
......@@ -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 {
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a.brackets:before,
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h1:hover > a.headerlink,
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......@@ -279,6 +289,12 @@ img.align-center, .figure.align-center, object.align-center {
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......@@ -287,6 +303,10 @@ img.align-center, .figure.align-center, object.align-center {
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......@@ -358,6 +378,11 @@ table.align-center {
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......@@ -391,6 +416,16 @@ table.citation td {
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......@@ -460,11 +495,58 @@ ol.upperroman {
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