{"id":3197,"date":"2023-07-01T23:26:16","date_gmt":"2023-07-01T14:26:16","guid":{"rendered":"https:\/\/plaza.umin.ac.jp\/~OIO\/?p=3197"},"modified":"2023-07-02T12:12:48","modified_gmt":"2023-07-02T03:12:48","slug":"%e3%82%b2%e3%83%8e%e3%83%a0%e3%83%af%e3%82%a4%e3%83%89%e9%96%a2%e9%80%a3%e8%a7%a3%e6%9e%90%ef%bc%88gwas%ef%bc%89%e3%81%ae%e3%83%9e%e3%83%b3%e3%83%8f%e3%83%83%e3%82%bf%e3%83%b3%e3%83%97%e3%83%ad","status":"publish","type":"post","link":"https:\/\/plaza.umin.ac.jp\/~OIO\/?p=3197","title":{"rendered":"\u30b2\u30ce\u30e0\u30ef\u30a4\u30c9\u95a2\u9023\u89e3\u6790\uff08GWAS\uff09\u306e\u30de\u30f3\u30cf\u30c3\u30bf\u30f3\u30d7\u30ed\u30c3\u30c8Manhattan plot"},"content":{"rendered":"<h1 id=\"firstHeading\" class=\"firstHeading mw-first-heading\"><span class=\"mw-page-title-main\">\u30b2\u30ce\u30e0\u30ef\u30a4\u30c9\u95a2\u9023\u89e3\u6790(GWAS)\u306e\u30de\u30f3\u30cf\u30c3\u30bf\u30f3\u30d7\u30ed\u30c3\u30c8<\/span><\/h1>\n<p>\u30a2\u30a4\u30ad\u30e3\u30c3\u30c1\u753b\u50cf\u306e\u3088\u3046\u306a\u56f3\u3092\u8ad6\u6587\u3067\u898b\u3066\u3044\u3066\u3001\u3069\u3046\u3084\u3063\u3066\u63cf\u3044\u305f\u3082\u306e\u3067\u4f55\u3092\u610f\u5473\u3059\u308b\u306e\u304b\u81ea\u5206\u3067\u3082\u3068\u30c7\u30fc\u30bf\u304b\u3089\u56f3\u3092\u63cf\u304d\u3064\u3064\u898b\u65b9\u3092\u5b66\u307c\u3046\u3068\u3044\u3046\u4e8b\u3067\u66f8\u7c4d\u3092\u958b\u304d\u306a\u304c\u3089\u8a66\u3057\u3066\u307f\u307e\u3057\u305f\u3002\u305d\u306e\u6642\u306e\u30c1\u30e7\u30b3\u3063\u3068\u3057\u305f\u5b66\u3073\u3092\u66f8\u304d\u7559\u3081\u305f\u5099\u5fd8\u9332\u3067\u3059\u3002<\/p>\n<p>#\u521d\u5fc3\u8005\u306b\u3088\u308b\u3084\u3063\u3066\u307f\u305f\u7cfb\u306e\u8a18\u4e8b<\/p>\n<h2>\u53c2\u8003\u306b\u3057\u305f\u66f8\u7c4d<\/h2>\n<p>\u53c2\u8003\u306b\u3057\u305f\u306e\u306f\u300c<a href=\"https:\/\/www.yodosha.co.jp\/yodobook\/book\/9784758120920\/\">\u30bc\u30ed\u304b\u3089\u5b9f\u8df5\u3059\u308b \u907a\u4f1d\u7d71\u8a08\u5b66\u30bb\u30df\u30ca\u30fc\u301c\u75be\u60a3\u3068\u30b2\u30ce\u30e0\u3092\u7d50\u3073\u3064\u3051\u308b<\/a>\u300d\u3068\u3044\u3046\u672c\u3067\u3059\u3002\u53c2\u8003\u3068\u3044\u3046\u304b\u3001\u3053\u306e\u30db\u30fc\u30e0\u30da\u30fc\u30b8\u306b\u66f8\u3044\u3066\u3044\u308b\u3053\u3068\u306f\u3001\u3053\u306e\u672c\u306b\u66f8\u304b\u308c\u3066\u3044\u308b\u3053\u3068\u3092\u305f\u3069\u3063\u305f\u3060\u3051\u3067\u3059\u3002\u66f8\u7c4d\u306b\u306fCGYWIN\u306e\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3001plink\u306e\u4f7f\u3044\u65b9\u304b\u3089\u3001\u30de\u30f3\u30cf\u30c3\u30bf\u30f3\u30d7\u30ed\u30c3\u30c8\u307e\u3067\u4e01\u5be7\u306b\u66f8\u304b\u308c\u3066\u3044\u307e\u3059\u306e\u3067\u3001\u3053\u306e\u66f8\u7c4d\u3092\u8aad\u3081\u3070\u79c1\u306e\u30db\u30fc\u30e0\u30da\u30fc\u30b8\u306f\u898b\u308b\u4fa1\u5024\u304c\u3042\u307e\u308a\u306a\u3044\u304b\u3082\u3057\u308c\u307e\u305b\u3093\u3002<\/p>\n<h2>R\u3067\u306e\u30d7\u30ed\u30c3\u30c8<\/h2>\n<p>\u3053\u3053\u3067\u3001\u4eca\u56de\u4f7f\u7528\u3057\u305fR\u306e\u30b9\u30af\u30ea\u30d7\u30c8\u3092\u63b2\u8f09\u3057\u3088\u3046\u3068\u601d\u3063\u3066\u3044\u305f\u306e\u3067\u3059\u304c\u3001\u305d\u306e\u30b9\u30af\u30ea\u30d7\u30c8\u3068\u3044\u3046\u306e\u304c\u4e0a\u8a18\u66f8\u7c4d\u3092\u8cfc\u5165\u3057\u305f\u3089\u30c0\u30a6\u30f3\u30ed\u30fc\u30c9\u3067\u304d\u308b\u3068\u3044\u3046\u30c7\u30fc\u30bf\u306e\u4e2d\u306b\u3042\u308b\u30b9\u30af\u30ea\u30d7\u30c8\u3067\u3001\u3054\u304f\u308f\u305a\u304b\u5909\u66f4\uff08\u30d5\u30a1\u30a4\u30eb\u683c\u7d0d\u30c7\u30a3\u30ec\u30af\u30c8\u30ea\u3084\u30c7\u30fc\u30bf\u30d5\u30a1\u30a4\u30eb\u540d\u3092\u5909\u66f4\uff09\u3057\u305f\u7a0b\u5ea6\u306a\u306e\u3067\u3001\u3055\u3059\u304c\u306b\u63b2\u8f09\u3057\u305f\u3089\u307e\u305a\u305d\u3046\u3060\u3068\u601d\u3044\u3068\u3069\u307e\u308a\u3001\u5225\u306e\u4f8b\u3067\u793a\u3057\u307e\u3059\u3002<\/p>\n<p>CRAN\u304b\u3089\u3001<a href=\"https:\/\/cran.r-project.org\/web\/packages\/qqman\/vignettes\/qqman.html\">R\u306e\u30d1\u30c3\u30b1\u30fc\u30b8qqman<\/a>\u3092\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3057\u3066\u3042\u308b\u3068\u3057\u3066\u6b21\u306b\u306a\u308a\u307e\u3059\u3002<\/p>\n<pre class=\"EnlighterJSRAW\" data-enlighter-language=\"generic\">library(qqman)\r\nmanhattan(gwasResults, chr=\"CHR\", bp=\"BP\", snp=\"SNP\", p=\"P\" )<\/pre>\n<p>gwasResults\u306f\u30d1\u30c3\u30b1\u30fc\u30b8qqman\u4ed8\u5c5e\u306e\u30c7\u30fc\u30bf\u3067\u3001\u6b21\u306e\u3088\u3046\u306bSNP\u306e\u540d\u79f0\u30fb\u67d3\u8272\u4f53\u30fb\u4f4d\u7f6e\u30fb\u8868\u73fe\u578b\u3068\u5f53\u8a72SNP\u3068\u306e\u95a2\u9023\u6027\u304c\u306a\u3044\u3068\u4eee\u5b9a\u3057\u305f\u5834\u5408\u306e\u78ba\u7387P\u5024\u306e\uff14\u9805\u76ee\u306e\u30c7\u30fc\u30bf\u304c16470\u884c\u7d9a\u304d\u307e\u3059\u3002<\/p>\n<p><img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/66c19942ab4ba346fdb64ccc04cde373.png\" alt=\"\" width=\"311\" height=\"393\" class=\"aligncenter size-full wp-image-3201\" srcset=\"https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/66c19942ab4ba346fdb64ccc04cde373.png 311w, https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/66c19942ab4ba346fdb64ccc04cde373-237x300.png 237w, https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/66c19942ab4ba346fdb64ccc04cde373-119x150.png 119w\" sizes=\"auto, (max-width: 311px) 100vw, 311px\" \/><\/p>\n<p>\u3067\u3001\u3053\u306e\u30b9\u30af\u30ea\u30d7\u30c8\u306e\u7d50\u679c\u306f\u6b21\u306e\u56f3\u306e\u3088\u3046\u306b\u306a\u308a\u307e\u3059\u3002<\/p>\n<p><img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot.png\" alt=\"\" width=\"882\" height=\"566\" class=\"aligncenter size-full wp-image-3203\" srcset=\"https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot.png 882w, https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot-300x193.png 300w, https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot-700x449.png 700w, https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot-150x96.png 150w, https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot-768x493.png 768w, https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot-500x321.png 500w, https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot-800x513.png 800w\" sizes=\"auto, (max-width: 882px) 100vw, 882px\" \/><\/p>\n<p>&nbsp;<\/p>\n<p>\u8272\u304c\u5bc2\u3057\u3044\u306e\u3067\u3001\u540c\u3058\u30c7\u30fc\u30bf\u3067\u30a6\u30af\u30e9\u30a4\u30ca\u3092\u601d\u308f\u305b\u308b\u30ab\u30e9\u30fc\u3067\u8868\u73fe\u3059\u308b\u3068<\/p>\n<pre class=\"EnlighterJSRAW\" data-enlighter-language=\"generic\"># Load the library\r\nlibrary(qqman)\r\n\r\n# Make the Manhattan plot on the gwasResults dataset\r\nmanhattan(gwasResults, chr=\"CHR\", bp=\"BP\", snp=\"SNP\", p=\"P\",  col = c(\"#0057B7\", \"#FFDD00\"))\r\n\r\n<\/pre>\n<p>\u6b21\u306e\u3088\u3046\u306b\u306a\u308a\u307e\u3059<\/p>\n<p><img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot01.png\" alt=\"\" width=\"882\" height=\"566\" class=\"aligncenter size-full wp-image-3205\" srcset=\"https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot01.png 882w, https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot01-300x193.png 300w, https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot01-700x449.png 700w, https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot01-150x96.png 150w, https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot01-768x493.png 768w, https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot01-500x321.png 500w, https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot01-800x513.png 800w\" sizes=\"auto, (max-width: 882px) 100vw, 882px\" \/><\/p>\n<p>\u56f3\u306e\u4e2d\u306eSNP\u3092\u8868\u793a\u3059\u308b\u306b\u306f\u3000<em>, annotatePval = 0.01\u3000<\/em>\u3092\u8ffd\u52a0\u3057\u307e\u3059<\/p>\n<pre class=\"EnlighterJSRAW\" data-enlighter-language=\"generic\"># Load the library\r\nlibrary(qqman)\r\n\r\n# Make the Manhattan plot on the gwasResults dataset\r\nmanhattan(gwasResults, chr=\"CHR\", bp=\"BP\", snp=\"SNP\", p=\"P\",  col = c(\"#0057B7\", \"#FFDD00\"), annotatePval = 0.01)<\/pre>\n<h2><img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot02.png\" alt=\"\" width=\"882\" height=\"566\" class=\"aligncenter size-full wp-image-3207\" srcset=\"https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot02.png 882w, https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot02-300x193.png 300w, https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot02-700x449.png 700w, https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot02-150x96.png 150w, https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot02-768x493.png 768w, https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot02-500x321.png 500w, https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot02-800x513.png 800w\" sizes=\"auto, (max-width: 882px) 100vw, 882px\" \/><\/h2>\n<h2>\u3082\u3046\u5c11\u3057\u56f3\u306b\u30d0\u30ea\u30a8\u30fc\u30b7\u30e7\u30f3\u3092<\/h2>\n<p>\uff13\u756a\u67d3\u8272\u4f53\u306e\u96c6\u4e2d\u3057\u3066\u3044\u304f\u3064\u3082\u306eSNP\u304c\u9ad8\u3044-log10(p)\u5024\u3092\u793a\u3059\u306e\u306b\u9802\u4e0a\u306e\u5909\u7570\u3057\u304b\u540d\u524d\u304c\u8868\u793a\u3055\u308c\u306a\u3044\u306e\u3067\u3000annotateTop = FALSE\u3000\u3068\u3044\u3046\u30aa\u30d7\u30b7\u30e7\u30f3\u3092\u3064\u3051\u3066\u307f\u307e\u3057\u305f\u3002<\/p>\n<pre class=\"EnlighterJSRAW\" data-enlighter-language=\"generic\"># Load the library\r\nlibrary(qqman)\r\n\r\n# Make the Manhattan plot on the gwasResults dataset\r\nmanhattan(subset(gwasResults, CHR == 3), chr=\"CHR\", bp=\"BP\", snp=\"SNP\", p=\"P\"\r\n          ,  col = c(\"#0057B7\", \"#FFDD00\"), annotatePval = 0.001\r\n          , annotateTop = FALSE, main = \"Chr 3\")\r\n<\/pre>\n<p><img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot-1.png\" alt=\"\" width=\"882\" height=\"581\" class=\"aligncenter size-full wp-image-3212\" srcset=\"https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot-1.png 882w, https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot-1-300x198.png 300w, https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot-1-700x461.png 700w, https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot-1-150x99.png 150w, https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot-1-768x506.png 768w, https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot-1-500x329.png 500w, https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot-1-800x527.png 800w\" sizes=\"auto, (max-width: 882px) 100vw, 882px\" \/><\/p>\n<p>\uff13\u756a\u76ee\u306e\u67d3\u8272\u4f53\u306b\u95a2\u9023\u306e\u3042\u308a\u305d\u3046\u306aSNP\u304c\u96c6\u4e2d\u3057\u3066\u3044\u308b\u3088\u3046\u306a\u306e\u30673\u756a\u76ee\u306esubset\u3092\u8868\u793a\u3057\u3066\u307f\u307e\u3059\u3002\u809d\u306f\u3000subset(gwasResults, CHR ==3)\u3000\u306e\u500b\u6240\u3067\u3059\u3002<\/p>\n<pre class=\"EnlighterJSRAW\" data-enlighter-language=\"generic\"># Load the library\r\nlibrary(qqman)\r\n\r\n# Make the Manhattan plot on the gwasResults dataset\r\nmanhattan(subset(gwasResults, CHR == 3), chr=\"CHR\", bp=\"BP\", snp=\"SNP\", p=\"P\"\r\n          ,  col = c(\"#0057B7\", \"#FFDD00\"), annotatePval = 0.001\r\n          , annotateTop = FALSE, main = \"Chr 3\")\r\n<\/pre>\n<p><img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot01-1.png\" alt=\"\" width=\"882\" height=\"581\" class=\"aligncenter size-full wp-image-3211\" srcset=\"https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot01-1.png 882w, https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot01-1-300x198.png 300w, https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot01-1-700x461.png 700w, https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot01-1-150x99.png 150w, https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot01-1-768x506.png 768w, https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot01-1-500x329.png 500w, https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot01-1-800x527.png 800w\" sizes=\"auto, (max-width: 882px) 100vw, 882px\" \/><\/p>\n<p>\u6c17\u306b\u306a\u308b\u3042\u305f\u308a\u3092\u3082\u3046\u5c11\u3057\u62e1\u5927\u3057\u307e\u3059<\/p>\n<pre class=\"EnlighterJSRAW\" data-enlighter-language=\"generic\"># Load the library\r\nlibrary(qqman)\r\n\r\n# Make the Manhattan plot on the gwasResults dataset\r\nmanhattan(subset(gwasResults, CHR == 3), chr=\"CHR\", bp=\"BP\", snp=\"SNP\", p=\"P\"\r\n          ,  col = c(\"#0057B7\", \"#FFDD00\"), annotatePval = 0.001\r\n          , annotateTop = FALSE, main = \"Chr 3\", xlim = c(200,500))<\/pre>\n<p><img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot02-1.png\" alt=\"\" width=\"882\" height=\"581\" class=\"aligncenter size-full wp-image-3210\" srcset=\"https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot02-1.png 882w, https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot02-1-300x198.png 300w, https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot02-1-700x461.png 700w, https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot02-1-150x99.png 150w, https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot02-1-768x506.png 768w, https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot02-1-500x329.png 500w, https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot02-1-800x527.png 800w\" sizes=\"auto, (max-width: 882px) 100vw, 882px\" \/><\/p>\n<p>&nbsp;<\/p>\n<h2>\u30c7\u30fc\u30bf\u306e\u4f5c\u6210<\/h2>\n<p>\u4e0a\u8a18\u306e\u4f5c\u56f3\u306f\u5358\u7d14\u3067\u3001\u5404Chromosome\u4e0a\u306e\u305d\u308c\u305e\u308c\u306e\u4f4d\u7f6e\u3067p\u5024\u3092\u30d7\u30ed\u30c3\u30c8\u3057\u305f\u3060\u3051\u306e\u3082\u306e\u306a\u306e\u3067\u3001\u7d50\u5c40\u306fp\u5024\u3092\u8a08\u7b97\u3057\u3066\u5927\u304d\u306a\u5916\u308c\u5024\uff08-&gt; association\uff09\u3092\u793a\u3059\u4f4d\u7f6e\u3092\u76ee\u8996\u3067\u78ba\u8a8d\u3057\u3084\u3059\u304f\u3057\u305f\u3082\u306e\u3060\u3068\u3044\u3046\u4e8b\u304c\u308f\u304b\u308a\u307e\u3057\u305f\u3002<\/p>\n<p>\u809d\u3068\u306a\u308b\u306e\u306fp\u5024\u306e\u8a08\u7b97\u306b\u306a\u308a\u307e\u3059\u3002\u305d\u308c\u3067\u306f\u3001p\u5024\u3092\u3069\u3046\u3084\u3063\u3066\u8a08\u7b97\u3057\u3066\u3044\u305f\u304b\u3068\u3044\u3046\u3068\u3001\u8907\u6570\u4eba\u306eSNP\u306e\u30c7\u30fc\u30bf\u3068\u3001\u305d\u308c\u305e\u308c\u306e\u30b5\u30f3\u30d7\u30eb\uff08\u306e\u4eba\uff09\u306e\u8208\u5473\u306e\u3042\u308b\u8868\u73fe\u578b\u306e\u30c7\u30fc\u30bf\u3092\u7528\u3044\u3066\u8868\u73fe\u578b\u3068\u7121\u95a2\u4fc2\u306aSNP\u304b\u8868\u73fe\u578b\u3068associate\u3057\u3066\u3044\u308bSNP\u304b\u3092\u8a08\u7b97\u3057\u3066\u3044\u307e\u3059\u3002<\/p>\n<p>plink.exe\u3000\uff08windows\u7528\uff09\u304c\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3055\u308c\u3066\u3044\u3066\u3001\u5192\u982d\u306e\u66f8\u7c4d\u306e\u4ed8\u9332\u306e\u30d5\u30a1\u30a4\u30eb\u30001KG_EUR_QC.bed, 1KG_EUR_QC.bim, 1KG_EUR_QC.fam \u3068\u304b\u306e\u30c7\u30fc\u30bf\u304c\u3042\u3063\u305f\u3068\u3057\u3066\u3001\u30b3\u30de\u30f3\u30c9\u30d7\u30ed\u30f3\u30d7\u30c8\u3067\u6b21\u3092\u5b9f\u65bd\u3057\u307e\u3057\u305f\u3002<\/p>\n<pre class=\"EnlighterJSRAW\" data-enlighter-language=\"generic\">plink.exe --bfile 1KG_EUR_QC --out 1KG_QC_Pheno1 --pheno phenotype1.txt --logistic --ci 0.95\r\n<\/pre>\n<p>\u4e0a\u8a18\u3067\u4f5c\u6210\u3055\u308c\u308b\u30d5\u30a1\u30a4\u30eb\u304b\u3089\u3001p\u5024\u7b49\u306e\u30c7\u30fc\u30bf\u3092\u62bd\u51fa\u3059\u308b\u306e\u306bawk\u3092\u4f7f\u3044\u307e\u3057\u305f\u3002awk\u3092\u4f7f\u3046\u306e\u306b\u3001MacOS\u3060\u3068awk\u306f\u30c7\u30d5\u30a9\u30eb\u30c8\u3067\u5165\u3063\u3066\u3044\u308b\u306e\u3067\u3059\u304c\u3001\u4eca\u56de\u306fwindows\u3092\u4f7f\u3044\u307e\u3057\u305f\u306e\u3067CYGWIN\u3067\u5b9f\u884c\u3057\u307e\u3057\u305f\u3002<\/p>\n<pre class=\"EnlighterJSRAW\" data-enlighter-language=\"generic\">awk '{print $2\"\\t\"($1*100000000000+$3)\"\\t\"$12}' 1KG_QC_Pheno1.assoc.logistic &gt; 1KG_QC_Pheno1.assoc.logistic.P.txt<\/pre>\n<p>\u3053\u306e\u51fa\u529b\u3067\u751f\u6210\u3055\u308c\u308b\u30001KG_QC_Pheno1.assoc.logistic.P.txt\u3000\u30d5\u30a1\u30a4\u30eb\u3092\u4e0a\u306e\u65b9\u3067\u8a18\u3057\u305fR\u30b9\u30af\u30ea\u30d7\u30c8\u306e\u30a4\u30f3\u30d7\u30c3\u30c8\u3068\u3059\u308b\u3053\u3068\u3067\u3001\u30de\u30f3\u30cf\u30c3\u30bf\u30f3\u30d7\u30ed\u30c3\u30c8\u3092\u63cf\u304f\u3053\u3068\u304c\u3067\u304d\u307e\u3057\u305f\u3002<\/p>\n<p>&nbsp;<\/p>\n<h2>\u516c\u958b\u30c7\u30fc\u30bf\u3092\u4f7f\u3063\u3066\u7df4\u7fd2<\/h2>\n<p>\u3055\u3089\u306a\u308b\u7df4\u7fd2\u7528\u3068\u3044\u3046\u4e8b\u3067\u300c<a href=\"https:\/\/humandbs.biosciencedbc.jp\/hum0014-v21#hum0014.v1.freq.v1\">\u5fc3\u7b4b\u6897\u585e1666\u75c7\u4f8b\u304a\u3088\u3073\u5bfe\u7167\u5065\u5e38\u80053198\u540d\u306eGWAS<\/a>\u300d\u30c7\u30fc\u30bf\u304c\u516c\u958b\u3055\u308c\u3066\u304a\u308a\u3001\u4f7f\u7528\u306b\u3064\u3044\u3066\u306e\u5236\u9650\u304c\u306a\u3044\u305f\u3081\u3053\u3061\u3089\u306e\u30c7\u30fc\u30bf\u3067\u8a66\u3057\u3066\u307f\u307e\u3057\u305f\u3002<br \/>\n\uff08\u5236\u9650\u304c\u306a\u3044\uff1dNBDC\u975e\u5236\u9650\u516c\u958b\u30c7\u30fc\u30bf\u3068\u306f\u3001\u30a2\u30af\u30bb\u30b9\u306b\u5236\u9650\u3092\u8a2d\u3051\u308b\u3053\u3068\u306a\u304f\u3001\u8ab0\u3067\u3082\u5229\u7528\u3059\u308b\u3053\u3068\u304c\u53ef\u80fd\u306a\u516c\u958b\u30c7\u30fc\u30bf\u3067\u3059\u3002\uff09<br \/>\n\u6b21\u306e\u30b5\u30a4\u30c8\u304b\u3089\u30c0\u30a6\u30f3\u30ed\u30fc\u30c9\u3057\u307e\u3057\u305f\u3002<\/p>\n<p>https:\/\/humandbs.biosciencedbc.jp\/<\/p>\n<p>\u300c<a href=\"https:\/\/www.yodosha.co.jp\/yodobook\/book\/9784758120920\/\">\u30bc\u30ed\u304b\u3089\u5b9f\u8df5\u3059\u308b \u907a\u4f1d\u7d71\u8a08\u5b66\u30bb\u30df\u30ca\u30fc\u301c\u75be\u60a3\u3068\u30b2\u30ce\u30e0\u3092\u7d50\u3073\u3064\u3051\u308b<\/a>\u300d\u306b\u5f93\u3063\u305f\u4f8b\u3067awk\u3067\u884c\u3063\u3063\u3066\u3044\u305f\u3001\u884c\u306e\u62bd\u51fa\u306e\u90e8\u5206\u306f\u3092sql\u3067\u884c\u3044\u307e\u3057\u305f\u3002<br \/>\n\u597d\u307f\u306e\u554f\u984c\u304b\u3082\u3057\u308c\u307e\u305b\u3093\u304c\u3001windows\u3067linux emulator\u307f\u305f\u3044\u306a\u306e\u3092\u7a3c\u50cd\u3055\u305b\u3066awk\u8d70\u3089\u305b\u308b\u3088\u308a\u3001Microsoft Access\u306eSQL\u3067\u62bd\u51fa\u3059\u308b\u306e\u304c\u7d20\u76f4\u306b\u958b\u767a\u3057\u3084\u3059\u3044\u3068\u611f\u3058\u307e\u3057\u305f\u3002<\/p>\n<pre class=\"EnlighterJSRAW\" data-enlighter-language=\"generic\">SELECT Release_L12vsUniv06_AllSample.[#SNPID] AS SNP, Release_L12vsUniv06_AllSample.chr AS chr, Release_L12vsUniv06_AllSample.chrloc AS location, Release_L12vsUniv06_AllSample.ptrend AS p INTO [0010 GWAS_results]\r\nFROM Release_L12vsUniv06_AllSample;<\/pre>\n<p>\u3067\u4f5c\u56f3\u306f\u6b21\u306e\u3088\u3046\u306b\u3057\u307e\u3057\u305f\u3002<\/p>\n<pre class=\"EnlighterJSRAW\" data-enlighter-language=\"generic\">library(readxl)\r\nlibrary(qqman)\r\n\r\nGWAS_results &lt;- read_excel(\"0010 GWAS_results.xlsx\")\r\nmanhattan(GWAS_results, chr=\"chr\", bp=\"location\", snp=\"SNP\", p=\"p\"\r\n          ,  col = c(\"#0057B7\", \"#FFDD00\"), annotatePval = 0.00001\r\n          ,  annotateTop = FALSE)\r\n\r\nmanhattan(subset(GWAS_results, chr == 12), chr=\"chr\", bp=\"location\", snp=\"SNP\", p=\"p\"\r\n          ,  col = c(\"#0057B7\", \"#FFDD00\"), annotatePval = 0.00001\r\n          ,  annotateTop = FALSE, xlim = c(1.1e+8, 1.12e+08))\r\n<\/pre>\n<p><img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot-2.png\" alt=\"\" width=\"2000\" height=\"1000\" class=\"aligncenter size-full wp-image-3214\" srcset=\"https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot-2.png 2000w, https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot-2-300x150.png 300w, https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot-2-700x350.png 700w, https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot-2-150x75.png 150w, https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot-2-768x384.png 768w, https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot-2-1536x768.png 1536w, https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot-2-500x250.png 500w, https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot-2-800x400.png 800w, https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot-2-1280x640.png 1280w, https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot-2-1920x960.png 1920w\" sizes=\"auto, (max-width: 2000px) 100vw, 2000px\" \/><\/p>\n<p>12\u756a\u67d3\u8272\u4f53\u306e3&#8217;\u5074\u306b\u4e0d\u5747\u8861\u304c\u96c6\u4e2d\u3057\u3066\u3044\u308b\u69d8\u306a\u306e\u3067\u305d\u306e\u3042\u305f\u308a\u3092\u62e1\u5927\u3057\u305f\u308a\u3057\u307e\u3057\u305f\u3002<\/p>\n<p><img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot01-2.png\" alt=\"\" width=\"2000\" height=\"1000\" class=\"aligncenter size-full wp-image-3215\" srcset=\"https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot01-2.png 2000w, https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot01-2-300x150.png 300w, https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot01-2-700x350.png 700w, https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot01-2-150x75.png 150w, https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot01-2-768x384.png 768w, https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot01-2-1536x768.png 1536w, https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot01-2-500x250.png 500w, https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot01-2-800x400.png 800w, https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot01-2-1280x640.png 1280w, https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/Rplot01-2-1920x960.png 1920w\" sizes=\"auto, (max-width: 2000px) 100vw, 2000px\" \/><\/p>\n<p>&nbsp;<\/p>\n<p>&nbsp;<\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u30b2\u30ce\u30e0\u30ef\u30a4\u30c9\u95a2\u9023\u89e3\u6790(GWAS)\u306e\u30de\u30f3\u30cf\u30c3\u30bf\u30f3\u30d7\u30ed\u30c3\u30c8 \u30a2\u30a4\u30ad\u30e3\u30c3\u30c1\u753b\u50cf\u306e\u3088\u3046\u306a\u56f3\u3092\u8ad6\u6587\u3067\u898b\u3066\u3044\u3066\u3001\u3069\u3046\u3084\u3063\u3066\u63cf\u3044\u305f\u3082\u306e\u3067\u4f55\u3092\u610f\u5473\u3059\u308b\u306e\u304b\u81ea\u5206\u3067\u3082\u3068\u30c7\u30fc\u30bf\u304b\u3089\u56f3\u3092\u63cf\u304d\u3064\u3064\u898b\u65b9\u3092\u5b66\u307c\u3046\u3068\u3044\u3046\u4e8b\u3067\u66f8\u7c4d\u3092\u958b\u304d\u306a\u304c\u3089\u8a66\u3057\u3066\u307f\u307e\u3057&#8230;<\/p>\n","protected":false},"author":1,"featured_media":3195,"comment_status":"open","ping_status":"open","sticky":true,"template":"","format":"standard","meta":{"_jetpack_memberships_contains_paid_content":false,"footnotes":""},"categories":[4],"tags":[],"class_list":["post-3197","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-science"],"jetpack_featured_media_url":"https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2023\/07\/1KG_QC_Pheno1.assoc_.logistic.P_position_P_15.png","jetpack_shortlink":"https:\/\/wp.me\/p9b6zl-Pz","jetpack_sharing_enabled":true,"_links":{"self":[{"href":"https:\/\/plaza.umin.ac.jp\/~OIO\/index.php?rest_route=\/wp\/v2\/posts\/3197","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/plaza.umin.ac.jp\/~OIO\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/plaza.umin.ac.jp\/~OIO\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/plaza.umin.ac.jp\/~OIO\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/plaza.umin.ac.jp\/~OIO\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=3197"}],"version-history":[{"count":0,"href":"https:\/\/plaza.umin.ac.jp\/~OIO\/index.php?rest_route=\/wp\/v2\/posts\/3197\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/plaza.umin.ac.jp\/~OIO\/index.php?rest_route=\/wp\/v2\/media\/3195"}],"wp:attachment":[{"href":"https:\/\/plaza.umin.ac.jp\/~OIO\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=3197"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/plaza.umin.ac.jp\/~OIO\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=3197"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/plaza.umin.ac.jp\/~OIO\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=3197"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}