{"id":37485,"date":"2011-02-09T13:37:33","date_gmt":"2011-02-09T21:37:33","guid":{"rendered":"http:\/\/blogs.discovermagazine.com\/gnxp\/?p=9807"},"modified":"2011-02-18T00:38:03","modified_gmt":"2011-02-18T08:38:03","slug":"inferring-and-visualizing-patterns-in-genomic-data","status":"publish","type":"post","link":"https:\/\/www.razib.com\/wordpress\/2011\/02\/09\/inferring-and-visualizing-patterns-in-genomic-data\/","title":{"rendered":"Inferring and visualizing patterns in genomic data"},"content":{"rendered":"<p>I&#8217;ve been playing around with <a href=\"http:\/\/www.genetics.ucla.edu\/software\/admixture\/\">ADMIXTURE<\/a> and <a href=\"http:\/\/genepath.med.harvard.edu\/~reich\/Software.htm\">EIGENSOFT<\/a> with the the HapMap data set along with a few friends &amp; family merged into it. It is interesting to see how the intuitive inferences you make from ADMIXTURE bar plots differ somewhat from PCA scatter plots. In any case, I&#8217;ve been posting some of the preliminary results on Facebook (in part because one of my friends is on Facebook and is curious about his own genetic background), and a friend who is a grad student pointed me to <a href=\"http:\/\/fisher.berkeley.edu\/structurama\/download.html\">Structurama<\/a>, which infers the best number of categories* (one can do cross-vaidation in ADMIXTURE). I&#8217;ve avoided <a href=\"http:\/\/pritch.bsd.uchicago.edu\/software.html\">STRUCTURE<\/a> because it&#8217;s computationally more intensive. Any other recommendations? Specifically, something <i>not<\/i> mentioned by <a href=\"http:\/\/dienekes.blogspot.com\/\">Dienekes<\/a> or <a href=\"http:\/\/bga101.blogspot.com\/\">David<\/a>.<\/p>\n<p>Below the fold is a taste of the games my computer has been up to overnight. K = 5 ancestral populations in ADMIXTURE. HapMap Utah whites, Tuscans, Mexicans, Beijing Chinese, in that order. The last 6 bars are: my father, my mother, and then four individuals of European ancestry, Euro 1, Euro 2, Euro 3, and Euro 4. After merging files and pruning founders and thinning the markers to reduce linkage disequilibrium I was left &#8230;<img loading=\"lazy\" decoding=\"async\" src=\"http:\/\/feeds.feedburner.com\/~r\/GeneExpressionBlog\/~4\/bhWnfMmqzOE\" height=\"1\" width=\"1\"\/><\/p>\n","protected":false},"excerpt":{"rendered":"<p>I&#8217;ve been playing around with ADMIXTURE and EIGENSOFT with the the HapMap data set along with a few friends &amp; family merged into it. It is interesting to see how the intuitive inferences you make from ADMIXTURE bar plots differ somewhat from &#8230;<\/p>\n","protected":false},"author":12,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[4,82,1118,1119],"tags":[],"class_list":["post-37485","post","type-post","status-publish","format-standard","hentry","category-genetics","category-genomics","category-software","category-visualization"],"_links":{"self":[{"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/posts\/37485","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=37485"}],"version-history":[{"count":6,"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/posts\/37485\/revisions"}],"predecessor-version":[{"id":37773,"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/posts\/37485\/revisions\/37773"}],"wp:attachment":[{"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/media?parent=37485"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/categories?post=37485"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/tags?post=37485"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}