{"id":1204,"date":"2007-09-21T19:18:31","date_gmt":"2007-09-21T17:18:31","guid":{"rendered":"http:\/\/www.wjst.de\/blog\/2007\/09\/21\/plink-again\/"},"modified":"2007-10-28T08:20:14","modified_gmt":"2007-10-28T06:20:14","slug":"tonk-plonk-and-plink","status":"publish","type":"post","link":"https:\/\/www.wjst.de\/blog\/sciencesurf\/2007\/09\/tonk-plonk-and-plink\/","title":{"rendered":"Tonk, Plonk and Plink"},"content":{"rendered":"<p>I have now used the <a href=\"https:\/\/www.wjst.de\/blog\/2007\/08\/13\/blink-plink\/\">PLINK<\/a> software package also for analysing family data. Again it is an excellent program that allows many new views on old data. I could run >20 traits all together on ~1000 SNPs in just a few seconds. There are only a few tweaks that I have already emailed to the author<!--more--> like<\/p>\n<blockquote><p>\n&#8211;hap-tdt option requires the flag &#8211;old-EM<br \/>\n&#8211;all-pheno option works for QTLs but not for categorial phenotypes<br \/>\n&#8211;lookup option needs to have its own output file<br \/>\n&#8211;epistasis option should work in families\n<\/p><\/blockquote>\n<p>The &#8220;downside&#8221; &#8211; there are so many new results from the German asthma family study, mostly additions to already published papers that will be  difficult to re-publish. For example VDR variants influence also lung function and bronchial hyperreactivity which has not been tested before.<br \/>\n<a href=\"https:\/\/www.wjst.de\/blog\/wp-content\/uploads\/2007\/09\/vdr.png\" title='' data-rel=\"key-image-0\" data-rl_title=\"\" data-rl_caption=\"\"><img src='https:\/\/www.wjst.de\/blog\/wp-content\/uploads\/2007\/09\/vdr.png' alt='vdr.png' \/><\/a><br \/>\nBTW &#8211; the title of this post goes back to an <a href=\"http:\/\/links.jstor.org\/sici?sici=0003-2638(196206)22%3A6%3C130%3ATPAP%3E2.0.CO%3B2-G\">article in JSTOR<\/a><\/p>\n\n<p>&nbsp;<\/p>\n<div class=\"bottom-note\">\n  <span class=\"mod1\">CC-BY-NC Science Surf , accessed 07.04.2026<\/span>\n <\/div>","protected":false},"excerpt":{"rendered":"<p>I have now used the PLINK software package also for analysing family data. Again it is an excellent program that allows many new views on old data. I could run >20 traits all together on ~1000 SNPs in just a few seconds. There are only a few tweaks that I have already emailed to the &hellip; <a href=\"https:\/\/www.wjst.de\/blog\/sciencesurf\/2007\/09\/tonk-plonk-and-plink\/\" class=\"more-link\">Continue reading <span class=\"screen-reader-text\">Tonk, Plonk and Plink<\/span> <span class=\"meta-nav\">&rarr;<\/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":[2,9,10],"tags":[1235,1236,1238,747,1237],"class_list":["post-1204","post","type-post","status-publish","format-standard","hentry","category-genetics-biology","category-computer-software","category-sunshine-vitamin","tag-bronchial_hyperreactivity","tag-epistasis","tag-hap","tag-phenotypes","tag-plink"],"_links":{"self":[{"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/posts\/1204","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/comments?post=1204"}],"version-history":[{"count":0,"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/posts\/1204\/revisions"}],"wp:attachment":[{"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/media?parent=1204"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/categories?post=1204"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/tags?post=1204"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}