{"id":38706,"date":"2011-03-15T23:45:12","date_gmt":"2011-03-16T07:45:12","guid":{"rendered":"http:\/\/blogs.discovermagazine.com\/gnxp\/?p=10342"},"modified":"2011-03-15T23:45:12","modified_gmt":"2011-03-16T07:45:12","slug":"eurasia-admixture-supervised-unsupervised","status":"publish","type":"post","link":"https:\/\/www.razib.com\/wordpress\/2011\/03\/15\/eurasia-admixture-supervised-unsupervised\/","title":{"rendered":"Eurasia, ADMIXTURE supervised & unsupervised"},"content":{"rendered":"

After yesterday’s post<\/a> I thought it might be useful to see how running ADMIXTURE in different modes would impact the outcomes. Probably the major reason I wish more people would use this software is that they’d see that this program is just<\/em> a program, and stop assuming its outputs to be divine writ.<\/strong> Over the years I’ve noticed a tendency of individuals anchoring to one specific plot in one specific paper as if it supported their argument definitively. Running ADMIXTURE or PCA plots via EIGENSOFT<\/a> makes you very aware of how useless this sort of stance is.<\/p>\n

Today I’ve limited the population set to be “South Asia-centric.” Specifically, there are only a few Middle Eastern, European, and East Asian populations, along with one African population. The goal is to figure out how different South Asian groups relate to these non-South Asian groups. First, I ran ADMIXTURE K = 2 to K = 9. Then, I ran ADMIXTURE in “supervised” mode for K = 9. Basically, I set nine populations as as “pure” references. They were:<\/p>\n

– Tamil Dalit
\n– French Basque
\n– Lithuanian
\n– Adygei
\n– Palestinian
\n– Buryat (Altaic region)
\n– Dai (South Asian)
\n– Papuan
\n– Luhya …<\/p>\n","protected":false},"excerpt":{"rendered":"

After yesterday’s post I thought it might be useful to see how running ADMIXTURE in different modes would impact the outcomes. Probably the major reason I wish more people would use this software is that they’d see that this program is jus…<\/p>\n","protected":false},"author":12,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[290,4,82],"tags":[],"class_list":["post-38706","post","type-post","status-publish","format-standard","hentry","category-admixture","category-genetics","category-genomics"],"_links":{"self":[{"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/posts\/38706","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/users\/12"}],"replies":[{"embeddable":true,"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/comments?post=38706"}],"version-history":[{"count":4,"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/posts\/38706\/revisions"}],"predecessor-version":[{"id":38953,"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/posts\/38706\/revisions\/38953"}],"wp:attachment":[{"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/media?parent=38706"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/categories?post=38706"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/tags?post=38706"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}