SNP genotype matrix for GWAS and Machine Learning analyses

<p><strong>SNP datasets used for GWAS and Machine Learning analyses</strong></p> <p>All datasets come from the easyGWAS website: <a href="https://easygwas.ethz.ch/down/1/">https://easygwas.ethz.ch/down/1/</a></p> <p>&nbsp;</p> <p><strong>=== Horton et al. 2012 ===</strong></p> <p><strong>1307 Arabidopsis genotypes x 214,057</strong> <strong>SNPs</strong></p> <p><strong>1) In the form of a genotype matrix </strong></p> <p>The file is called <a href="https://zenodo.org/api/files/d862e79f-02f2-4176-9b8e-04e48a2cf72c/horton2012.raw?versionId=2b05fb8d-b486-4f00-b7bf-bb024b892dc9">Horton2012.raw</a></p> <p><a href="https://www.nature.com/articles/ng.1042">https://www.nature.com/articles/ng.1042</a></p> <p>Preview of the first lines and columns:</p> <p>FID&nbsp;&nbsp; &nbsp;Chr1_657_T&nbsp;&nbsp; &nbsp;Chr1_3102_G&nbsp;&nbsp; &nbsp;Chr1_4648_A&nbsp;&nbsp; &nbsp;Chr1_4880_T&nbsp;&nbsp; &nbsp;Chr1_5975_G&nbsp;&nbsp; &nbsp;Chr1_6063_T&nbsp;&nbsp; &nbsp;Chr1_6449_C<br> 9381&nbsp;&nbsp; &nbsp;2&nbsp;&nbsp; &nbsp;2&nbsp;&nbsp; &nbsp;2&nbsp;&nbsp; &nbsp;0&nbsp;&nbsp; &nbsp;0&nbsp;&nbsp; &nbsp;0&nbsp;&nbsp; &nbsp;0<br> 9380&nbsp;&nbsp; &nbsp;0&nbsp;&nbsp; &nbsp;0&nbsp;&nbsp; &nbsp;0&nbsp;&nbsp; &nbsp;0&nbsp;&nbsp; &nbsp;0&nbsp;&nbsp; &nbsp;0&nbsp;&nbsp; &nbsp;2<br> 9378&nbsp;&nbsp; &nbsp;2&nbsp;&nbsp; &nbsp;2&nbsp;&nbsp; &nbsp;2&nbsp;&nbsp; &nbsp;0&nbsp;&nbsp; &nbsp;0&nbsp;&nbsp; &nbsp;0&nbsp;&nbsp; &nbsp;0<br> 9371&nbsp;&nbsp; &nbsp;2&nbsp;&nbsp; &nbsp;2&nbsp;&nbsp; &nbsp;2&nbsp;&nbsp; &nbsp;0&nbsp;&nbsp; &nbsp;0&nbsp;&nbsp; &nbsp;0&nbsp;&nbsp; &nbsp;0<br> 9367&nbsp;&nbsp; &nbsp;0&nbsp;&nbsp; &nbsp;0&nbsp;&nbsp; &nbsp;0&nbsp;&nbsp; &nbsp;2&nbsp;&nbsp; &nbsp;0&nbsp;&nbsp; &nbsp;0&nbsp;&nbsp; &nbsp;0<br> 9363&nbsp;&nbsp; &nbsp;2&nbsp;&nbsp; &nbsp;2&nbsp;&nbsp; &nbsp;2&nbsp;&nbsp; &nbsp;0&nbsp;&nbsp; &nbsp;0&nbsp;&nbsp; &nbsp;0&nbsp;&nbsp; &nbsp;0<br> 9356&nbsp;&nbsp; &nbsp;0&nbsp;&nbsp; &nbsp;2&nbsp;&nbsp; &nbsp;2&nbsp;&nbsp; &nbsp;0&nbsp;&nbsp; &nbsp;0&nbsp;&nbsp; &nbsp;0&nbsp;&nbsp; &nbsp;0<br> 9355&nbsp;&nbsp; &nbsp;2&nbsp;&nbsp; &nbsp;2&nbsp;&nbsp; &nbsp;2&nbsp;&nbsp; &nbsp;0&nbsp;&nbsp; &nbsp;0&nbsp;&nbsp; &nbsp;0&nbsp;&nbsp; &nbsp;0<br> 9354&nbsp;&nbsp; &nbsp;2&nbsp;&nbsp; &nbsp;2&nbsp;&nbsp; &nbsp;2&nbsp;&nbsp; &nbsp;0&nbsp;&nbsp; &nbsp;0&nbsp;&nbsp; &nbsp;0&nbsp;&nbsp; &nbsp;0</p> <p>...etc...</p> <p>PLINK 1.9 was used to convert the .ped and .map file to a .raw format with:&nbsp;</p> <pre><code class="language-bash">plink --file original_data/genotype --recodeA --tab</code></pre> <p>Genotypes are encoded as 0, 1 or 2 with:</p> <pre> SNP SNP_A --- ----- A A -&gt; 0 A C -&gt; 1 C C -&gt; 2 0 0 -&gt; NA </pre> <p>Then only the Family ID was kept (same as individual ID) and other columns (Paternal ID, Maternal ID, Sex, Phenotype) were removed.</p> <p>The corresponding PLINK manual page used is here: <a href="https://zzz.bwh.harvard.edu/plink/dataman.shtml#recode">https://zzz.bwh.harvard.edu/plink/dataman.shtml#recode</a></p> <p><strong>1) In the form of set of files compatible with PLINK out of the box</strong></p> <p>The archive file is called <a href="https://zenodo.org/api/files/b34fd40e-2db1-47b0-92c8-0ad51ad92d46/AtPolyDB_call_method_75_Horton2012.tar.gz">AtPolyDB_call_method_75_Horton2012.tar.gz</a> and contains three files:</p> <ul> <li>genotype.ped: pedigree information from the 1307 ecotypes</li> <li>genotype.map: the SNP positions on the genome</li> <li>phenotypes.pheno: the phenotype value of the 1307 ecotypes</li> </ul> <p>&nbsp;</p>