{"id":435,"date":"2025-07-10T20:08:18","date_gmt":"2025-07-10T20:08:18","guid":{"rendered":"https:\/\/open.qtlmax.com\/guide\/?p=435"},"modified":"2025-07-11T00:40:35","modified_gmt":"2025-07-11T00:40:35","slug":"performing-a-genomic-control-computation","status":"publish","type":"post","link":"https:\/\/open.qtlmax.com\/guide\/index.php\/2025\/07\/10\/performing-a-genomic-control-computation\/","title":{"rendered":"How to perform a genomic control computation"},"content":{"rendered":"\n

Figure 1 displays the QQ plot generated from the P-values<\/strong> obtained by performing GLM-GWAS calculations with demo data. As you can see, the points on the plot significantly deviate from the red diagonal line, moving sharply upwards and to the right with a very large slope. This phenomenon is referred to as genomic inflation<\/strong>.<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

(Figure 1)<\/p>\n\n\n\n

Figure 2 shows the Genomic Control tab after completing the genomic control calculation. This was done by selecting the “pvalues<\/strong>” file (a result file generated after either GLM-GWAS or LMM-GWAS analysis) and clicking the [Execute]<\/strong> button. The file generated from the genomic control calculation is saved in the same folder as the input file (pvalues<\/strong>).<\/p>\n\n\n\n

Here’s an explanation of the files created by the genomic control calculation:<\/p>\n\n\n\n

    \n
  1. gc_pvalues<\/strong>: This file contains the P-values<\/strong> that have been adjusted through the genomic control calculation.<\/li>\n\n\n\n
  2. lambda<\/strong>: This value (ranging from 0-1) indicates the strength of genomic inflation<\/strong>. A lambda value closer to 1 means the genomic inflation is stronger. Conversely, a value closer to 0 indicates that the P-values better follow a chi-squared distribution with 1 degree of freedom.<\/li>\n<\/ol>\n\n\n
    \n
    \"\"<\/figure>\n<\/div>\n\n\n

    (Figure 2)<\/p>\n\n\n\n

    Figure 3 shows the project folder after the genomic inflation calculation. You can see that the gc_pvalues<\/strong> file and the lambda<\/strong> file are now present alongside the existing GWAS result files.<\/p>\n\n\n

    \n
    \"\"\/<\/figure>\n<\/div>\n\n\n

    (Figure 3)<\/p>\n\n\n\n

    Figure 4 shows the newly drawn QQ plot using the adjusted P-values<\/strong> contained in the “gc_pvalues<\/strong>” file. As you can see, the P-values now follow the red diagonal line relatively well.
    <\/p>\n\n\n\n

    \"\"<\/figure>\n\n\n\n

    (Figure 4)<\/p>\n\n\n\n

    Figure 5 shows the lambda value<\/strong> (lambda GC = 6.515145) calculated during the genomic inflation process.<\/p>\n\n\n

    \n
    \"\"\/<\/figure>\n<\/div>\n\n\n

    (Figure 5)<\/p>\n\n\n\n

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

    Figure 1 displays the QQ plot generated from the P-values obtained by performing GLM-GWAS calculations with demo data. As you can see, the points on the plot significantly deviate from the red diagonal line, moving sharply upwards and to the right with a very large slope. This phenomenon is referred to as genomic inflation. (Figure […]<\/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-435","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\/435","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=435"}],"version-history":[{"count":10,"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/posts\/435\/revisions"}],"predecessor-version":[{"id":634,"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/posts\/435\/revisions\/634"}],"wp:attachment":[{"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/media?parent=435"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/categories?post=435"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/open.qtlmax.com\/guide\/index.php\/wp-json\/wp\/v2\/tags?post=435"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}