{"id":645,"date":"2025-07-11T00:56:17","date_gmt":"2025-07-11T00:56:17","guid":{"rendered":"https:\/\/open.qtlmax.com\/guide\/?p=645"},"modified":"2025-07-11T01:05:27","modified_gmt":"2025-07-11T01:05:27","slug":"gwas-procedure-generalized-linear-model","status":"publish","type":"post","link":"https:\/\/open.qtlmax.com\/guide\/index.php\/2025\/07\/11\/gwas-procedure-generalized-linear-model\/","title":{"rendered":"GWAS procedure (Generalized linear model)"},"content":{"rendered":"\n<p>In GLM-GWAS calculations, the imputation step is optional, not mandatory. In this regard, the GLM-GWAS calculation procedure provides the following two filtering options: (1) Missing ID %: Removes samples with a missing rate higher than the set value (0-1).(2) Missing SNP %: Removes SNP markers with a missing rate higher than the set value (0-1).<\/p>\n\n\n\n<p>Meanwhile, in LMM-GWAS calculations, both of the above two filtering options are performed during the imputation process.<\/p>\n\n\n\n<p>Figure 1 shows the <strong>GLM-GWAS tab page<\/strong> when it&#8217;s selected. When you choose a <strong>phenotype file<\/strong> written in CSV format, the header values of that phenotype file will be listed in the &#8220;Columns&#8221; text box.<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img loading=\"lazy\" decoding=\"async\" width=\"1007\" height=\"961\" src=\"https:\/\/open.qtlmax.com\/guide\/wp-content\/uploads\/2025\/07\/QTLmax-5.0_023.png\" alt=\"\" class=\"wp-image-651\" srcset=\"https:\/\/open.qtlmax.com\/guide\/wp-content\/uploads\/2025\/07\/QTLmax-5.0_023.png 1007w, https:\/\/open.qtlmax.com\/guide\/wp-content\/uploads\/2025\/07\/QTLmax-5.0_023-300x286.png 300w, https:\/\/open.qtlmax.com\/guide\/wp-content\/uploads\/2025\/07\/QTLmax-5.0_023-768x733.png 768w\" sizes=\"auto, (max-width: 1007px) 100vw, 1007px\" \/><\/figure>\n\n\n\n<p>(Figure 1)<\/p>\n\n\n\n<p>In addition to the filtering options mentioned above, the GLM-GWAS tab page requires a few other settings, and each configuration method is as follows:<\/p>\n\n\n\n<ol start=\"1\" class=\"wp-block-list\">\n<li>Send the header value that specifies the <strong>sample<\/strong> to the &#8220;Sample column&#8221; text box.<\/li>\n\n\n\n<li>Send the header value that specifies the <strong>phenotype value<\/strong> to the &#8220;Phenotype column&#8221; text box.<\/li>\n\n\n\n<li>Send the header values that specify the <strong>PCA values<\/strong> to the &#8220;Covariate (continuous)&#8221; text box. (e.g., PC1, PC2, PC3)<\/li>\n<\/ol>\n\n\n\n<figure class=\"wp-block-image size-full\"><img loading=\"lazy\" decoding=\"async\" width=\"1007\" height=\"961\" src=\"https:\/\/open.qtlmax.com\/guide\/wp-content\/uploads\/2025\/07\/QTLmax-5.0_024.png\" alt=\"\" class=\"wp-image-656\" srcset=\"https:\/\/open.qtlmax.com\/guide\/wp-content\/uploads\/2025\/07\/QTLmax-5.0_024.png 1007w, https:\/\/open.qtlmax.com\/guide\/wp-content\/uploads\/2025\/07\/QTLmax-5.0_024-300x286.png 300w, https:\/\/open.qtlmax.com\/guide\/wp-content\/uploads\/2025\/07\/QTLmax-5.0_024-768x733.png 768w\" sizes=\"auto, (max-width: 1007px) 100vw, 1007px\" \/><\/figure>\n\n\n\n<p>(Figure 2)<\/p>\n\n\n\n<p>The path to the GLM-GWAS calculation result file is as follows:<\/p>\n\n\n\n<p class=\"has-text-align-center\"><strong>Working directory > Project > Trait folder<\/strong><\/p>\n","protected":false},"excerpt":{"rendered":"<p>In GLM-GWAS calculations, the imputation step is optional, not mandatory. In this regard, the GLM-GWAS calculation procedure provides the following two filtering options: (1) Missing ID %: Removes samples with a missing rate higher than the set value (0-1).(2) Missing SNP %: Removes SNP markers with a missing rate higher than the set value (0-1). [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_bbp_topic_count":0,"_bbp_reply_count":0,"_bbp_total_topic_count":0,"_bbp_total_reply_count":0,"_bbp_voice_count":0,"_bbp_anonymous_reply_count":0,"_bbp_topic_count_hidden":0,"_bbp_reply_count_hidden":0,"_bbp_forum_subforum_count":0,"footnotes":""},"categories":[1],"tags":[],"class_list":["post-645","post","type-post","status-publish","format-standard","hentry","category-guide"],"_links":{"self":[{"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/posts\/645","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/comments?post=645"}],"version-history":[{"count":8,"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/posts\/645\/revisions"}],"predecessor-version":[{"id":660,"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/posts\/645\/revisions\/660"}],"wp:attachment":[{"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/media?parent=645"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/categories?post=645"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/tags?post=645"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}