{"id":302,"date":"2025-07-03T17:43:55","date_gmt":"2025-07-03T17:43:55","guid":{"rendered":"https:\/\/open.qtlmax.com\/guide\/?p=302"},"modified":"2025-07-11T00:57:00","modified_gmt":"2025-07-11T00:57:00","slug":"lmm-gwas-steps","status":"publish","type":"post","link":"https:\/\/open.qtlmax.com\/guide\/index.php\/2025\/07\/03\/lmm-gwas-steps\/","title":{"rendered":"GWAS steps (linear mixed model)"},"content":{"rendered":"\n

1. Imputation<\/a>
<\/strong>\u00a0\u00a0\u00a0\u00a0(QTLmax \u25b6 Preprocess \u25b6 Imputation)<\/p>\n\n\n\n

2. PCA computation<\/a>
<\/strong>    (QTLmax \u25b6 Genetic analytics \u25b6 Association \u25b6 Population studies \u25b6 ADMIXTURE)<\/p>\n\n\n\n

3. Genetic similarity matrix computation<\/a>
<\/strong>    (QTLmax \u25b6 Genetic analytics \u25b6 Association \u25b6 Population studies \u25b6 ADMIXTURE)<\/p>\n\n\n\n

4. Merging phenotype and PCA tables<\/a>
<\/strong>    (QTLmax Workbench \u25b6 Miscellaneous tools \u25b6 DataPro)<\/p>\n\n\n\n

5. LMM-GWAS<\/a>
<\/strong>    (QTLmax \u25b6 Genetic analytics \u25b6 Association \u25b6 Linear mixed model \u25b6 GWAS)<\/p>\n\n\n\n

6. Genomic control<\/a> (Use this in case that genomic inflation is observed.)
<\/strong>    (QTLmax \u25b6 Genetic analytics \u25b6 Association \u25b6 Genomic control)<\/p>\n\n\n\n

7. Manhattan plotting<\/a>
<\/strong>    (QTLmax Workbench \u25b6 Graph studio \u25b6 Manhattan plot)<\/p>\n\n\n\n

8. QQ plotting<\/a>
<\/strong>    (QTLmax Workbench \u25b6 Graph studio \u25b6 QQ plot)<\/p>\n\n\n\n

<\/p>\n","protected":false},"excerpt":{"rendered":"

1. Imputation\u00a0\u00a0\u00a0\u00a0(QTLmax \u25b6 Preprocess \u25b6 Imputation) 2. PCA computation     (QTLmax \u25b6 Genetic analytics \u25b6 Association \u25b6 Population studies \u25b6 ADMIXTURE) 3. Genetic similarity matrix computation    (QTLmax \u25b6 Genetic analytics \u25b6 Association \u25b6 Population studies \u25b6 ADMIXTURE) 4. Merging phenotype and PCA tables    (QTLmax Workbench \u25b6 Miscellaneous tools \u25b6 DataPro) 5. LMM-GWAS    (QTLmax \u25b6 Genetic analytics \u25b6 Association \u25b6 […]<\/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-302","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\/302","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=302"}],"version-history":[{"count":25,"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/posts\/302\/revisions"}],"predecessor-version":[{"id":647,"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/posts\/302\/revisions\/647"}],"wp:attachment":[{"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/media?parent=302"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/categories?post=302"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/tags?post=302"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}