{"id":596,"date":"2021-11-28T22:27:13","date_gmt":"2021-11-28T22:27:13","guid":{"rendered":"http:\/\/darwin.eeb.uconn.edu\/uncommon-ground\/eeb348\/?p=596"},"modified":"2021-11-28T22:27:13","modified_gmt":"2021-11-28T22:27:13","slug":"lab-exercise-on-genome-wide-association-analysis","status":"publish","type":"post","link":"https:\/\/darwin.eeb.uconn.edu\/uncommon-ground\/eeb348\/2021\/11\/28\/lab-exercise-on-genome-wide-association-analysis\/","title":{"rendered":"Lab exercise on genome-wide association analysis"},"content":{"rendered":"\n<p class=\"has-drop-cap\">It took me a bit longer to make sure the data and associated scripts were performing the way I wanted them to, but the lab exercise for week 13 is now posted. You&#8217;ll be running a genome-wide association analysis on a subset of data collected in an analysis of gypsy moths (<em>Lymantria dispar<\/em>). This is only an example. You can look at the Stan code if you want. If you do, you&#8217;ll see that it&#8217;s just the linear regression that we&#8217;ll discuss in class on Thursday with some magic added to take care of the relatedness among individuals. If you were doing a real GWAS, I wouldn&#8217;t recommend using this script. I&#8217;d recommend using <a href=\"https:\/\/github.com\/genetics-statistics\/GEMMA\" data-type=\"URL\" data-id=\"https:\/\/github.com\/genetics-statistics\/GEMMA\">GEMMA<\/a> or something like it that was built by experts in GWAS specifically for the purpose of GWAS. There are a lot of things to be careful about that aren&#8217;t built into these simple scripts, but they illustrate the principle so that you can get a sense of how GWAS might be used in your own research.<\/p>\n\n\n\n<p>As usual, you can find a link to the lab from the Lecture Schedule page (or you can in a few minutes when I get it posted) or from the link here.<\/p>\n\n\n\n<ul class=\"wp-block-list\"><li><a href=\"http:\/\/darwin.eeb.uconn.edu\/eeb348-resources\/Lab13.nb.html\" data-type=\"URL\" data-id=\"http:\/\/darwin.eeb.uconn.edu\/eeb348-resources\/Lab13.nb.html\">GWAS in gypsy moths<\/a><\/li><\/ul>\n\n\n\n<p><\/p>\n","protected":false},"excerpt":{"rendered":"<p>It took me a bit longer to make sure the data and associated scripts were performing the way I wanted them to, but the lab exercise for week 13 is now posted. You&#8217;ll be running a genome-wide association analysis on a subset of data collected in an analysis of gypsy moths (Lymantria dispar). This is &hellip; <\/p>\n<p class=\"link-more\"><a href=\"https:\/\/darwin.eeb.uconn.edu\/uncommon-ground\/eeb348\/2021\/11\/28\/lab-exercise-on-genome-wide-association-analysis\/\" class=\"more-link\">Continue reading<span class=\"screen-reader-text\"> &#8220;Lab exercise on genome-wide association analysis&#8221;<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"class_list":["post-596","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"_links":{"self":[{"href":"https:\/\/darwin.eeb.uconn.edu\/uncommon-ground\/eeb348\/wp-json\/wp\/v2\/posts\/596","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/darwin.eeb.uconn.edu\/uncommon-ground\/eeb348\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/darwin.eeb.uconn.edu\/uncommon-ground\/eeb348\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/darwin.eeb.uconn.edu\/uncommon-ground\/eeb348\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/darwin.eeb.uconn.edu\/uncommon-ground\/eeb348\/wp-json\/wp\/v2\/comments?post=596"}],"version-history":[{"count":1,"href":"https:\/\/darwin.eeb.uconn.edu\/uncommon-ground\/eeb348\/wp-json\/wp\/v2\/posts\/596\/revisions"}],"predecessor-version":[{"id":597,"href":"https:\/\/darwin.eeb.uconn.edu\/uncommon-ground\/eeb348\/wp-json\/wp\/v2\/posts\/596\/revisions\/597"}],"wp:attachment":[{"href":"https:\/\/darwin.eeb.uconn.edu\/uncommon-ground\/eeb348\/wp-json\/wp\/v2\/media?parent=596"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/darwin.eeb.uconn.edu\/uncommon-ground\/eeb348\/wp-json\/wp\/v2\/categories?post=596"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/darwin.eeb.uconn.edu\/uncommon-ground\/eeb348\/wp-json\/wp\/v2\/tags?post=596"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}