{"id":155,"date":"2013-12-07T20:02:38","date_gmt":"2013-12-07T20:02:38","guid":{"rendered":"http:\/\/pop-gen.eu\/wordpress\/?page_id=155"},"modified":"2024-07-01T20:06:38","modified_gmt":"2024-07-01T20:06:38","slug":"combine-omegaplus-and-sweed-thresholds-from-simulations","status":"publish","type":"page","link":"https:\/\/pop-gen.eu\/wordpress\/selective-sweep-analysis-pipelines\/combine-omegaplus-and-sweed-thresholds-from-simulations","title":{"rendered":"Combine OmegaPlus and SweeD &#8211; thresholds from simulations"},"content":{"rendered":"<p>Download the .tar.gz file that contains all necessary file for this demonstration.<\/p>\n<p><a href=\"http:\/\/pop-gen.eu\/wordpress\/wp-content\/uploads\/2013\/12\/combine_plots_simOutliers.tar.gz\">combine_plots_simOutliers.tar.gz<\/a><\/p>\n<p>I will demonstrate how to run the R script\u00a0<strong>combine_plots_sims.R<\/strong> which <strong>combines the results of OmegaPlus with SweeD and detects the common outlier<\/strong>s <em>based on neutral simulations<\/em>. Additionally, given a gff file with gene annotations it prints out the outlier genes.<\/p>\n<p><span style=\"color: #ff0000;\">Please use the latest versions of SweeD (&gt;= 3.2.3) and OmegaPlus (&gt;=2.2.4). These versions facilitate the import of the analysis results into R.<\/span><\/p>\n<p><span style=\"color: #ff0000;\">Please open and inspect the combine_plots_sims.R. Probably you will need to modify the file names.<\/span><\/p>\n<p>The scirpt combine_plots_sims.R performs the following steps<\/p>\n<ol>\n<li>performs neutral simulations. The user must set the variable &#8220;simulations&#8221; to 1 and also set the correct demographic model.<\/li>\n<li>Based on the neutral simulations, it computes a threshold for the SweeD and for the OmegaPlus<\/li>\n<li>It detects the points from a <em>real<\/em> (observation) dataset (not simulated), that are over the threshold<\/li>\n<li>creates plots of OmegaPlus, SweeD and a combined plot<\/li>\n<li>Given a gff file with the coordinates of genes on the genome, it finds out the outlier genes<\/li>\n<\/ol>\n<p>To execute the script <strong>combine_plots_sims.R<\/strong>, you can either use the command line<\/p>\n<pre> R CMD BATCH .\/combine_plots_sims.R<\/pre>\n<p>or open it with emacs+ess or rstudio to execute it line-by-line.<\/p>\n<p><strong>Results<\/strong><\/p>\n<p>The final result may look similar to the one below:<\/p>\n<p><a href=\"http:\/\/pop-gen.eu\/wordpress\/wp-content\/uploads\/2013\/12\/figureOutliers.png\"><img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-medium wp-image-169\" alt=\"figureOutliers\" src=\"http:\/\/pop-gen.eu\/wordpress\/wp-content\/uploads\/2013\/12\/figureOutliers-250x300.png\" width=\"250\" height=\"300\" srcset=\"https:\/\/pop-gen.eu\/wordpress\/wp-content\/uploads\/2013\/12\/figureOutliers-250x300.png 250w, https:\/\/pop-gen.eu\/wordpress\/wp-content\/uploads\/2013\/12\/figureOutliers-853x1024.png 853w, https:\/\/pop-gen.eu\/wordpress\/wp-content\/uploads\/2013\/12\/figureOutliers.png 1000w\" sizes=\"auto, (max-width: 250px) 100vw, 250px\" \/><\/a><\/p>\n<p>In this figure, the left panel represents the score profile of SweeD and OmegaPlus; gray are the points where the score is calculated. Red are the\u00a0<em>common\u00a0<\/em>outliers based on neutral simulations. On the right panel you can see the combined plot OmegaPlus vs SweeD.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Download the .tar.gz file that contains all necessary file for this demonstration. combine_plots_simOutliers.tar.gz I will demonstrate how to run the R script\u00a0combine_plots_sims.R which combines the results of OmegaPlus with SweeD and detects the common outliers based on neutral simulations. Additionally, given a gff file with gene annotations it prints out the outlier genes. Please use &hellip; <\/p>\n<p class=\"link-more\"><a href=\"https:\/\/pop-gen.eu\/wordpress\/selective-sweep-analysis-pipelines\/combine-omegaplus-and-sweed-thresholds-from-simulations\" class=\"more-link\">Continue reading<span class=\"screen-reader-text\"> &#8220;Combine OmegaPlus and SweeD &#8211; thresholds from simulations&#8221;<\/span><\/a><\/p>\n","protected":false},"author":4,"featured_media":0,"parent":89,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-155","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/pop-gen.eu\/wordpress\/wp-json\/wp\/v2\/pages\/155","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/pop-gen.eu\/wordpress\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/pop-gen.eu\/wordpress\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/pop-gen.eu\/wordpress\/wp-json\/wp\/v2\/users\/4"}],"replies":[{"embeddable":true,"href":"https:\/\/pop-gen.eu\/wordpress\/wp-json\/wp\/v2\/comments?post=155"}],"version-history":[{"count":10,"href":"https:\/\/pop-gen.eu\/wordpress\/wp-json\/wp\/v2\/pages\/155\/revisions"}],"predecessor-version":[{"id":171,"href":"https:\/\/pop-gen.eu\/wordpress\/wp-json\/wp\/v2\/pages\/155\/revisions\/171"}],"up":[{"embeddable":true,"href":"https:\/\/pop-gen.eu\/wordpress\/wp-json\/wp\/v2\/pages\/89"}],"wp:attachment":[{"href":"https:\/\/pop-gen.eu\/wordpress\/wp-json\/wp\/v2\/media?parent=155"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}