{"id":148,"date":"2024-03-09T18:53:44","date_gmt":"2024-03-09T10:53:44","guid":{"rendered":"http:\/\/www.alearnerlin.top\/?p=148"},"modified":"2024-03-09T18:57:38","modified_gmt":"2024-03-09T10:57:38","slug":"summary-data-based-mendelian-randomization-analysis","status":"publish","type":"post","link":"http:\/\/www.alearnerlin.top\/index.php\/2024\/03\/09\/summary-data-based-mendelian-randomization-analysis\/","title":{"rendered":"Summary data-based Mendelian Randomization analysis"},"content":{"rendered":"<h1>SMR\u7b80\u4ecb\u4ee5\u53ca\u4ee3\u7801\u5b9e\u64cd<\/h1>\n<h1>\u4e00\u3001\u7b80\u4ecb<\/h1>\n<p><strong>SMR<\/strong>\u662f\u7531\u897f\u6e56\u5927\u5b66\u6768\u5065\u6559\u6388\u56e2\u961f\u5f00\u53d1\u5e76\u652f\u6301\u7684\u4e00\u4e2a\u8fdb\u884cSMR\u4ee5\u53caHEIDI\u68c0\u9a8c\u7684\u8f6f\u4ef6\u5de5\u5177\u3002\u5176\u5b98\u65b9\u7f51\u5740\u662f<a href=\"https:\/\/yanglab.westlake.edu.cn\/software\/smr\/#Overview\" title=\"SMR\">SMR<\/a>\uff0c\u5176\u4e2d\u5305\u542b\u4e86\u5bf9SMR\u7684\u8be6\u7ec6\u4ecb\u7ecd\u4ee5\u53ca\u64cd\u4f5c\u6559\u7a0b\u3002<\/p>\n<p><strong>SMR(Summary data-based Mendelian Randomization analysis)<\/strong>,\u5176\u6838\u5fc3\u601d\u60f3\u5c31\u662f\u5229\u7528eQTL\u6570\u636e\u5bf9\u67d0\u4e9bphenotype\u8fdb\u884c<strong>MR\u5206\u6790<\/strong>\uff0c\u5f97\u5230\u9633\u6027\u7ed3\u679c\u540e\uff0c\u56e0\u4e3aeQTL\u672c\u8eab\u5bf9\u57fa\u56e0\u8868\u8fbe\u7684\u5f71\u54cd\uff0c\u5f97\u5230\u7ed3\u679c\uff1a\u57fa\u56e0\u8868\u8fbe\u5f71\u54cdphenotype\u3002\u5728\u5b98\u7f51\u91cc\u9762\u4e5f\u653e\u51fa\u4e86\u76f8\u5173\u7684\u6587\u732e\uff0c<a href=\"http:\/\/https:\/\/www.nature.com\/articles\/ng.3538\" title=\"\u6587\u7ae0\u5730\u5740\">\u6587\u7ae0\u5730\u5740<\/a>\uff0c\u5efa\u8bae\u4e00\u8bfb\uff0c\u80fd\u589e\u52a0\u5bf9SMR\u672c\u8eab\u7684\u7406\u89e3\u3002<\/p>\n<p>\u4e0b\u9762\u662fSMR\u7684\u64cd\u4f5c\u6b65\u9aa4\uff1a<\/p>\n<h3>\u9884\u5907\u6b65\u9aa41\uff1a\u8f6f\u4ef6\u4e0b\u8f7d<\/h3>\n<ul>\n<li>\u8fdb\u5165SMR\u7f51\u7ad9\u540e,\u5728Download\u91cc\u9762\u9009\u62e9\u4e0b\u8f7d\u3002\u8fd9\u91cc\u6211\u4f7f\u7528Windows\u7248\u672c\u8fdb\u884c\u6f14\u793a\uff0cwin\u7248\u672c\u64cd\u4f5c\u7b80\u5355\uff0c\u5bf9\u4e8e\u4e0d\u4f1aLinux\u7684\u4eba\u6765\u8bf4\u975e\u5e38\u53cb\u597d\uff0c\u6240\u4ee5\u4e0b\u8f7dwin\u7248\u672c<br \/>\n<div class='fancybox-wrapper lazyload-container-unload' data-fancybox='post-images' href='http:\/\/www.alearnerlin.top\/wp-content\/uploads\/2024\/03\/d42473-020-00264-z_18111600.jpg'><img class=\"lazyload lazyload-style-1\" src=\"data:image\/svg+xml;base64,PCEtLUFyZ29uTG9hZGluZy0tPgo8c3ZnIHdpZHRoPSIxIiBoZWlnaHQ9IjEiIHhtbG5zPSJodHRwOi8vd3d3LnczLm9yZy8yMDAwL3N2ZyIgc3Ryb2tlPSIjZmZmZmZmMDAiPjxnPjwvZz4KPC9zdmc+\"  decoding=\"async\" data-original=\"http:\/\/www.alearnerlin.top\/wp-content\/uploads\/2024\/03\/d42473-020-00264-z_18111600.jpg\" src=\"data:image\/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAEAAAABCAYAAAAfFcSJAAAAAXNSR0IArs4c6QAAAARnQU1BAACxjwv8YQUAAAAJcEhZcwAADsQAAA7EAZUrDhsAAAANSURBVBhXYzh8+PB\/AAffA0nNPuCLAAAAAElFTkSuQmCC\" alt=\"\" \/><\/div><\/li>\n<li>\u4e0b\u8f7d\u597d\u4e4b\u540e\u9009\u62e9\u4e00\u4e2a\u5408\u9002\u7684\u4f4d\u7f6e\u89e3\u538b\u5373\u53ef\uff0c\u89e3\u538b\u540e\u5e94\u8be5\u80fd\u770b\u5230\u4e0b\u9762\u8fd9\u4e09\u4e2a\u6587\u4ef6\u3002\u5176\u4e2d.exe\u540e\u7f00\u7684\u5c31\u662f\u6211\u9700\u8981\u4f7f\u7528\u7684SMR\u8f6f\u4ef6\uff0c\u4f46\u662f\u8fd9\u662f\u4e00\u4e2a\u547d\u4ee4\u884c\u5de5\u5177\u662f\u4e0d\u80fd\u76f4\u63a5\u6253\u5f00\u7684\u3002<br \/>\n<div class='fancybox-wrapper lazyload-container-unload' data-fancybox='post-images' href='http:\/\/www.alearnerlin.top\/wp-content\/uploads\/2024\/03\/\u5fae\u4fe1\u622a\u56fe_20240302193356.jpg'><img class=\"lazyload lazyload-style-1\" src=\"data:image\/svg+xml;base64,PCEtLUFyZ29uTG9hZGluZy0tPgo8c3ZnIHdpZHRoPSIxIiBoZWlnaHQ9IjEiIHhtbG5zPSJodHRwOi8vd3d3LnczLm9yZy8yMDAwL3N2ZyIgc3Ryb2tlPSIjZmZmZmZmMDAiPjxnPjwvZz4KPC9zdmc+\"  decoding=\"async\" data-original=\"http:\/\/www.alearnerlin.top\/wp-content\/uploads\/2024\/03\/\u5fae\u4fe1\u622a\u56fe_20240302193356.jpg\" src=\"data:image\/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAEAAAABCAYAAAAfFcSJAAAAAXNSR0IArs4c6QAAAARnQU1BAACxjwv8YQUAAAAJcEhZcwAADsQAAA7EAZUrDhsAAAANSURBVBhXYzh8+PB\/AAffA0nNPuCLAAAAAElFTkSuQmCC\" alt=\"\" \/><\/div><\/p>\n<h3>\u9884\u5907\u6b65\u9aa42\uff1a\u6570\u636e\u51c6\u5907<\/h3>\n<\/li>\n<li>\u5728\u5b8c\u6210SMR\u8f6f\u4ef6\u4e0b\u8f7d\u4e4b\u540e\uff0c\u6211\u4eec\u9700\u8981\u51c6\u5907\u6211\u4eec\u5206\u6790\u6240\u9700\u8981\u7684\u6570\u636e\u3002\u5176\u4e2d\u5305\u62ec\uff1aGWAS\u6570\u636e\u4ee5\u53caeQTL\u6570\u636e\u3002<br \/>\n<strong>eQTL\u6570\u636e\u51c6\u5907<\/strong><\/li>\n<li>eQTL\u6570\u636e\u5728SMR\u5b98\u65b9\u7f51\u7ad9\u63d0\u4f9b\u4e86\u5f88\u591a\u6570\u636e\u91cf\u5f88\u5927\u7684\u6570\u636e\u3002\u4e0b\u8f7d\u901f\u5ea6\u5f88\u5feb\uff0c\u5206\u6790\u8005\u53ef\u4ee5\u6309\u7167\u81ea\u5df1\u7684\u9700\u6c42\u8fdb\u884c\u9009\u62e9\u3002eQTLGen\u4e5f\u63d0\u4f9b\u4e86SMR\u683c\u5f0f\u7684\u8840\u6db2\u6837\u672c\u7684eQTL\u6570\u636e\u3002<br \/>\n<div class='fancybox-wrapper lazyload-container-unload' data-fancybox='post-images' href='http:\/\/www.alearnerlin.top\/wp-content\/uploads\/2024\/03\/\u5fae\u4fe1\u622a\u56fe_20240302193931.jpg'><img class=\"lazyload lazyload-style-1\" src=\"data:image\/svg+xml;base64,PCEtLUFyZ29uTG9hZGluZy0tPgo8c3ZnIHdpZHRoPSIxIiBoZWlnaHQ9IjEiIHhtbG5zPSJodHRwOi8vd3d3LnczLm9yZy8yMDAwL3N2ZyIgc3Ryb2tlPSIjZmZmZmZmMDAiPjxnPjwvZz4KPC9zdmc+\"  decoding=\"async\" data-original=\"http:\/\/www.alearnerlin.top\/wp-content\/uploads\/2024\/03\/\u5fae\u4fe1\u622a\u56fe_20240302193931.jpg\" src=\"data:image\/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAEAAAABCAYAAAAfFcSJAAAAAXNSR0IArs4c6QAAAARnQU1BAACxjwv8YQUAAAAJcEhZcwAADsQAAA7EAZUrDhsAAAANSURBVBhXYzh8+PB\/AAffA0nNPuCLAAAAAElFTkSuQmCC\" alt=\"\" \/><\/div><br \/>\n<div class='fancybox-wrapper lazyload-container-unload' data-fancybox='post-images' href='http:\/\/www.alearnerlin.top\/wp-content\/uploads\/2024\/03\/\u5fae\u4fe1\u622a\u56fe_20240302194200.jpg'><img class=\"lazyload lazyload-style-1\" src=\"data:image\/svg+xml;base64,PCEtLUFyZ29uTG9hZGluZy0tPgo8c3ZnIHdpZHRoPSIxIiBoZWlnaHQ9IjEiIHhtbG5zPSJodHRwOi8vd3d3LnczLm9yZy8yMDAwL3N2ZyIgc3Ryb2tlPSIjZmZmZmZmMDAiPjxnPjwvZz4KPC9zdmc+\"  decoding=\"async\" data-original=\"http:\/\/www.alearnerlin.top\/wp-content\/uploads\/2024\/03\/\u5fae\u4fe1\u622a\u56fe_20240302194200.jpg\" src=\"data:image\/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAEAAAABCAYAAAAfFcSJAAAAAXNSR0IArs4c6QAAAARnQU1BAACxjwv8YQUAAAAJcEhZcwAADsQAAA7EAZUrDhsAAAANSURBVBhXYzh8+PB\/AAffA0nNPuCLAAAAAElFTkSuQmCC\" alt=\"\" \/><\/div><\/li>\n<li>\u6211\u4eec\u4e0b\u8f7d\u597d\u4e4b\u540e\u4f1a\u53d1\u73b0\uff0ceQTL\u6570\u636e\u5206\u522b\u662f\u7531\u4e09\u4e2a\u6587\u4ef6\u7ec4\u6210\uff0c\u5305\u62ec.BESD\u6587\u4ef6 .EPI\u6587\u4ef6 .ESI\u6587\u4ef6\u3002\u5c06\u5176\u4e0eSMR\u7a0b\u5e8f\u653e\u5230\u540c\u4e00\u4e2a\u6587\u4ef6\u5939\u4e2d\uff0c\u5982\u4e0b\u56fe\u6240\u793a\uff08\u4ee5\u5916\u5468\u8840eQTLGen\u4e3a\u4f8b\uff09\u3002\u8fd9\u4e2a\u5c31\u662fSMR\u683c\u5f0f\u7684eQTL\u6587\u4ef6\uff0c\u540e\u9762\u76f4\u63a5\u5206\u6790\u5c31\u53ef\u4ee5\u4e86\u3002<br \/>\n<div class='fancybox-wrapper lazyload-container-unload' data-fancybox='post-images' href='http:\/\/www.alearnerlin.top\/wp-content\/uploads\/2024\/03\/\u5fae\u4fe1\u622a\u56fe_20240302194634.jpg'><img class=\"lazyload lazyload-style-1\" src=\"data:image\/svg+xml;base64,PCEtLUFyZ29uTG9hZGluZy0tPgo8c3ZnIHdpZHRoPSIxIiBoZWlnaHQ9IjEiIHhtbG5zPSJodHRwOi8vd3d3LnczLm9yZy8yMDAwL3N2ZyIgc3Ryb2tlPSIjZmZmZmZmMDAiPjxnPjwvZz4KPC9zdmc+\"  decoding=\"async\" data-original=\"http:\/\/www.alearnerlin.top\/wp-content\/uploads\/2024\/03\/\u5fae\u4fe1\u622a\u56fe_20240302194634.jpg\" src=\"data:image\/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAEAAAABCAYAAAAfFcSJAAAAAXNSR0IArs4c6QAAAARnQU1BAACxjwv8YQUAAAAJcEhZcwAADsQAAA7EAZUrDhsAAAANSURBVBhXYzh8+PB\/AAffA0nNPuCLAAAAAElFTkSuQmCC\" alt=\"\" \/><\/div><\/p>\n<hr \/>\n<p><strong>GWAS\u6570\u636e\u51c6\u5907<\/strong><br \/>\n-eQTL\u6570\u636e\u51c6\u5907\u597d\u4e4b\u540e\uff0c\u6211\u4eec\u7ee7\u7eed\u51c6\u5907GWAS\u6570\u636e\u3002GWAS\u6570\u636e\u5728\u505a\u5b5f\u5fb7\u5c14\u968f\u673a\u5316\u5206\u6790\u7684\u65f6\u5019\uff0c\u5927\u5bb6\u5f80\u5f80\u76f4\u63a5\u5728TwoSampleMR\u5305\u901a\u8fc7IEU\u7684API\u5728R\u4e2d\u76f4\u63a5\u8bfb\u53d6\uff0c\u8fd9\u91cc\u56e0\u4e3a\u662f\u672c\u5730\u5206\u6790\uff0c\u6240\u4ee5\u9700\u8981\u4e0b\u8f7dGWAS\u6570\u636e\u5e76\u8f6c\u6362\u4e3aTXT\u6587\u4ef6\u8fdb\u884c\u5206\u6790\u3002<\/p>\n<\/li>\n<li>\u6211\u4eec\u4e0b\u8f7dIEU opengwas\u7684\u6570\u636e\u4e3e\u4f8b\uff0cIEU opengwas\u7684\u6570\u636e\u683c\u5f0f\u662fvcf\u683c\u5f0f\uff0c\u4e5f\u662f\u5927\u591a\u6570GWAS\u6570\u636e\u7684\u5e38\u7528\u683c\u5f0f\u3002<\/li>\n<li>\u6211\u9009\u62e9\u4e86eczemas,\u4e5f\u5c31\u662f\u6e7f\u75b9\u7684GWAS\u6570\u636e\u8fdb\u884c\u5904\u7406\uff0c\u5904\u7406\u7684\u8fc7\u7a0b\u4e5f\u662f\u975e\u5e38\u7b80\u5355\u3002\u51e0\u884c\u4ee3\u7801\u5c31\u53ef\u4ee5\u641e\u5b9a\u3002\u4ee3\u7801\u9644\u4e0a\u3002\n<pre><code class=\"language-r\">setwd(&quot;D:\\\\MR\\\\SMR\\\\Blog&quot;)\nlibrary(VariantAnnotation)\nlibrary(gwasglue)\ngwasdata&lt;-readVcf(&quot;ieu-a-996.vcf.gz&quot;)\ngwasdata&lt;-gwasvcf_to_TwoSampleMR(gwasdata,&quot;outcome&quot;)\ngwasdata&lt;-data.frame(gwasdata$SNP,\n                 gwasdata$effect_allele.outcome,\n                 gwasdata$other_allele.outcome,\n                 gwasdata$eaf.outcome,\n                 gwasdata$beta.outcome,\n                 gwasdata$se.outcome,\n                 gwasdata$pval.outcome,\n                 gwasdata$samplesize.outcome)\ncolnames(gwasdata)&lt;-c(&quot;snp&quot;,&quot;A1&quot;,&quot;A2&quot;,&quot;freq&quot;,&quot;b&quot;,&quot;se&quot;,&quot;p&quot;,&quot;n&quot;)\nwrite.table(gwasdata,&quot;gwas.txt&quot;,quote = FALSE,row.names = FALSE)<\/code><\/pre>\n<h2>\u5b8c\u6210\u4e0a\u8ff0\u6b65\u9aa4\u4e4b\u540e\uff0c\u6211\u4eec\u5c31\u5f97\u5230\u81ea\u5df1\u7684GWAS\u6587\u4ef6\u4e86\uff0c\u540c\u6837\u7684\u4e5f\u662f\u548cSMR\u7a0b\u5e8f\u653e\u5230\u540c\u4e00\u4e2a\u76ee\u5f55\u4e0b\u3002<\/h2>\n<p><strong>LD\u6587\u4ef6\u51c6\u5907<\/strong><\/p>\n<\/li>\n<li>\u9664GWAS\u6570\u636e\u4ee5\u53caeQTL\u6570\u636e\u4ee5\u5916\uff0c\u8fd8\u9700\u8981\u53c2\u8003\u57fa\u56e0\u7ec4\u6587\u4ef6\uff0c\u8fd9\u91cc\u6211\u662f\u4f7f\u7528\u7684\u7f51\u4e0a\u7684\u8d44\u6e90\u7684\uff0c\u5e94\u8be5\u662f\u4e00\u4e2aIEU\u7684\u670d\u52a1\u5668\u63d0\u4f9b\u7684\uff0c\u8fd9\u91cc\u9644\u4e0a\u4e0b\u8f7d\u94fe\u63a5\uff0c<a href=\"http:\/\/fileserve.mrcieu.ac.uk\/ld\/1kg.v3.tgz\" title=\"LD\u6587\u4ef6\u4e0b\u8f7d\">LD\u6587\u4ef6\u4e0b\u8f7d<\/a>\u5927\u5bb6\u4e5f\u53ef\u4ee5\u76f4\u63a5\u53bb<a href=\"http:\/\/www.internationalgenome.org\/data\" title=\"1000 Genome Projects\">1000 Genome Projects<\/a>\u7684\u5b98\u65b9\u7f51\u7ad9\u4e0b\u8f7d\uff0c\u76ee\u524d\u7b14\u8005\u8fd8\u6ca1\u641e\u6e05\u695a\u600e\u4e48\u4f7f\u7528\uff0c\u540e\u671f\u5f04\u660e\u767d\u4e86\u4e5f\u8bb8\u4f1a\u51fa\u4e00\u4e2a\u6559\u7a0b\u3002\u6bd5\u7adf\u8fd9\u4e2a\u9879\u76ee\u8fd8\u662f\u5f88\u91cd\u8981\u7684\u3002<\/li>\n<li>\u4e0b\u8f7d\u597d\u4e4b\u540e\uff0c\u91cc\u9762\u5e94\u8be5\u662f\u5305\u542b\u591a\u4e2a\u4eba\u79cd\u7684\u6570\u636e\uff0c\u4e00\u822c\u4f7f\u7528\u6b27\u6d32\u4eba\u79cd\u7684\u6570\u636e\uff0c\u9700\u8981\u5c06\u89e3\u538b\u7684\u6570\u636e\uff0c\u653e\u5230\u4e00\u4e2a\u7279\u5b9a\u7684\u8def\u5f84\u4e0b\uff08\u4e0d\u9700\u8981\u653e\u5230SMR\u7a0b\u5e8f\u8def\u5f84\u4e0b\uff0c\u907f\u514d\u5f71\u54cd\u5176\u4ed6\u5206\u6790\u4f7f\u7528LD\u6587\u4ef6\uff09<br \/>\n\u6211\u7684LD\u6587\u4ef6\u8def\u5f84\u662f<code>D:\\EUR_ref\\1kg.v3\\EUR<\/code>\u9700\u8981\u4f7f\u7528EUR\u65f6\uff0c\u5c31\u5728\u8def\u5f84\u7684\u6700\u540e\u52a0\u4e0a\u6307\u5b9a\u7684\u4eba\u79cd\uff0c\u5982\u679c\u4f7f\u7528\u4e9a\u6d32\u4eba\u7fa4\u7684\u8bdd\uff0c\u90a3\u4e48\u8def\u5f84\u5c31\u662f<code>D:\\EUR_ref\\1kg.v3\\EAS<\/code>\u3002<div class='fancybox-wrapper lazyload-container-unload' data-fancybox='post-images' href='http:\/\/www.alearnerlin.top\/wp-content\/uploads\/2024\/03\/\u5fae\u4fe1\u622a\u56fe_20240303095241.jpg'><img class=\"lazyload lazyload-style-1\" src=\"data:image\/svg+xml;base64,PCEtLUFyZ29uTG9hZGluZy0tPgo8c3ZnIHdpZHRoPSIxIiBoZWlnaHQ9IjEiIHhtbG5zPSJodHRwOi8vd3d3LnczLm9yZy8yMDAwL3N2ZyIgc3Ryb2tlPSIjZmZmZmZmMDAiPjxnPjwvZz4KPC9zdmc+\"  decoding=\"async\" data-original=\"http:\/\/www.alearnerlin.top\/wp-content\/uploads\/2024\/03\/\u5fae\u4fe1\u622a\u56fe_20240303095241.jpg\" src=\"data:image\/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAEAAAABCAYAAAAfFcSJAAAAAXNSR0IArs4c6QAAAARnQU1BAACxjwv8YQUAAAAJcEhZcwAADsQAAA7EAZUrDhsAAAANSURBVBhXYzh8+PB\/AAffA0nNPuCLAAAAAElFTkSuQmCC\" alt=\"\" \/><\/div><br \/>\n<strong>\u6570\u636e\u51c6\u5907\u5b8c\u6210\uff01\uff01\u73b0\u5728SMR\u7a0b\u5e8f\u6587\u4ef6\u4e0b\u5e94\u8be5\u5305\u542b\u5982\u4e0b\u6587\u4ef6\uff0c\u8bf7\u81ea\u67e5<\/strong><br \/>\n<div class='fancybox-wrapper lazyload-container-unload' data-fancybox='post-images' href='http:\/\/www.alearnerlin.top\/wp-content\/uploads\/2024\/03\/\u5fae\u4fe1\u622a\u56fe_20240303095611.jpg'><img class=\"lazyload lazyload-style-1\" src=\"data:image\/svg+xml;base64,PCEtLUFyZ29uTG9hZGluZy0tPgo8c3ZnIHdpZHRoPSIxIiBoZWlnaHQ9IjEiIHhtbG5zPSJodHRwOi8vd3d3LnczLm9yZy8yMDAwL3N2ZyIgc3Ryb2tlPSIjZmZmZmZmMDAiPjxnPjwvZz4KPC9zdmc+\"  decoding=\"async\" data-original=\"http:\/\/www.alearnerlin.top\/wp-content\/uploads\/2024\/03\/\u5fae\u4fe1\u622a\u56fe_20240303095611.jpg\" src=\"data:image\/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAEAAAABCAYAAAAfFcSJAAAAAXNSR0IArs4c6QAAAARnQU1BAACxjwv8YQUAAAAJcEhZcwAADsQAAA7EAZUrDhsAAAANSURBVBhXYzh8+PB\/AAffA0nNPuCLAAAAAElFTkSuQmCC\" alt=\"\" \/><\/div><\/p>\n<h3>SMR\u5206\u6790<\/h3>\n<h4>1. win\uff0bR\u8f93\u5165cmd\uff0c\u6253\u5f00\u7ec8\u7aef\u547d\u4ee4\u884c<\/h4>\n<p>\u56e0\u4e3aSMR\u662f\u4e00\u4e2a\u6ca1\u6709\u56fe\u5f62\u5316\u754c\u9762\u7684\u8f6f\u4ef6\uff0c\u6240\u4ee5\u9700\u8981\u76f4\u63a5\u4f7f\u7528\u547d\u4ee4\u884c\u7a97\u53e3\u8fdb\u884c\u4f7f\u7528\u3002win\u952e\uff0bR\u8f93\u5165cmd\uff0c\u53ef\u4ee5\u5feb\u901f\u6253\u5f00\u547d\u4ee4\u884c\u7a97\u53e3<\/p>\n<h4>2. \u5207\u6362\u5230SMR\u7a0b\u5e8f\u76ee\u5f55<\/h4>\n<p><code>D:<\/code>\u7531\u4e8e\u4e0d\u80fd\u8de8\u76d8\u7b26\u5207\u6362\u76ee\u5f55\uff0c\u9996\u5148\u5207\u6362\u5230D\u76d8\uff0c<code>cd D:\\MR\\SMR\\smr-1.3.1-win-x86_64\\smr-1.3.1-win-x86_64<\/code>\u5207\u6362\u5230\u6307\u5b9a\u76ee\u5f55\uff0c\u8f93\u5165<code>smr-1.3.1-win.exe<\/code>\u56de\u8f66\u4e4b\u540e\u5c31\u8fdb\u5165SMR\u8f6f\u4ef6\u4e86\u3002<br \/>\n<div class='fancybox-wrapper lazyload-container-unload' data-fancybox='post-images' href='http:\/\/www.alearnerlin.top\/wp-content\/uploads\/2024\/03\/\u5fae\u4fe1\u622a\u56fe_20240303100518.jpg'><img class=\"lazyload lazyload-style-1\" src=\"data:image\/svg+xml;base64,PCEtLUFyZ29uTG9hZGluZy0tPgo8c3ZnIHdpZHRoPSIxIiBoZWlnaHQ9IjEiIHhtbG5zPSJodHRwOi8vd3d3LnczLm9yZy8yMDAwL3N2ZyIgc3Ryb2tlPSIjZmZmZmZmMDAiPjxnPjwvZz4KPC9zdmc+\"  decoding=\"async\" data-original=\"http:\/\/www.alearnerlin.top\/wp-content\/uploads\/2024\/03\/\u5fae\u4fe1\u622a\u56fe_20240303100518.jpg\" src=\"data:image\/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAEAAAABCAYAAAAfFcSJAAAAAXNSR0IArs4c6QAAAARnQU1BAACxjwv8YQUAAAAJcEhZcwAADsQAAA7EAZUrDhsAAAANSURBVBhXYzh8+PB\/AAffA0nNPuCLAAAAAElFTkSuQmCC\" alt=\"\" \/><\/div><\/p>\n<h4>3. SMR\u5206\u6790<\/h4>\n<p>\u6309\u7167\u5b98\u7f51\u7ed9\u7684\u6559\u7a0b\uff0c\u6539\u6210\u6211\u4eec\u81ea\u5df1\u7684\u53c2\u6570\u548c\u6570\u636e\uff0c\u76f4\u63a5\u8fdb\u884c\u5206\u6790\u3002<br \/>\n<code>smr --bfile mydata --gwas-summary mygwas.ma --beqtl-summary myeqtl --out mysmr --thread-num 10<\/code><\/p>\n<\/li>\n<li>smr \u8fd9\u91cc\u5b98\u7f51\u4e0a\u5199\u7684smr\uff0c\u4e2a\u4eba\u5b9e\u6d4b\u5e94\u8be5\u5f97\u7528\u7a0b\u5e8f\u540d\uff0c\u6211\u7684\u538b\u7f29\u5305\u91cc\u9762\u7684\u7a0b\u5e8f\u540d\u662f<code>smr-1.3.1-win.exe<\/code><\/li>\n<li>bfile \u4e2a\u4eba\u7684LD\u6587\u4ef6\u8def\u5f84\uff0c\u6211\u7684\u662f\uff0cD:\\EUR_ref\\1kg.v3\\EUR<\/li>\n<li>gwas-summary mygwas.ma   ---gwas\u6587\u4ef6\u540d<\/li>\n<li>beqtl-summary  myeqtl --eqtl\u6587\u4ef6\u540d\uff08\u65e0\u540e\u7f00\uff0c\u4e09\u4e2a\u6587\u4ef6\uff09<\/li>\n<li>thread-num \u6307\u5b9a OpenMP \u7ebf\u7a0b\u6570 \u5e76\u884c\u8ba1\u7b97\u3002\u9ed8\u8ba4\u503c\u4e3a 1\u3002\u4e2a\u4eba\u7406\u89e3\u53ef\u80fd\u662f\u548c\u8ba1\u7b97\u673a\u8ba1\u7b97\u76f8\u5173\u7684\u53c2\u6570\u3002\u8fd9\u91cc\u6309\u7167\u7f51\u4e0a\u8d44\u6599\uff0c\u4f7f\u752810<\/li>\n<li>out mysmr --SMR\u7ed3\u679c\u6587\u4ef6<br \/>\n\u7b80\u5355\u7684\u4fee\u6539\u4e4b\u540e\u5c31\u5f97\u5230\u4e86\u81ea\u5df1\u4f7f\u7528\u7684\u547d\u4ee4\u4e86<br \/>\n<code>smr-1.3.1-win.exe --bfile D:\\EUR_ref\\1kg.v3\\EUR  --gwas-summary gwas.txt --beqtl-summary cis-eQTLs-full_eQTLGen_AF_incl_nr_formatted_20191212.new.txt_besd-dense --out SMR_outcome --thread-num 10 --diff-freq-prop 0.92 <\/code><br \/>\n<strong>diff-freq-prop<\/strong> \u53c2\u8003\u77e5\u4e4e\u4e0a\u4e00\u4f4d\u535a\u4e3b\u7684\u6559\u7a0b\uff0c<a href=\"http:\/\/zhuanlan.zhihu.com\/p\/659654054\" title=\"\u77e5\u4e4e\u94fe\u63a5\">\u77e5\u4e4e\u94fe\u63a5<\/a>\uff0c\u4ed6\u8bbe\u7f6e\u4e86diff-freq-prop\u5c31\u662f\u57fa\u56e0\u9891\u7387\u7684\u9608\u503c\uff0c\u8fd9\u4e00\u6b65\u5927\u5bb6\u53ef\u4ee5\u6309\u7167\u81ea\u5df1\u7684\u9700\u6c42\u53bb\u505a\uff0c\u6216\u8005\u591a\u6362\u51e0\u79cd\u4e0d\u540c\u7684\u9608\u503c\u8fdb\u884c\u5c1d\u8bd5\u3002\u4e4b\u540e\u5173\u4e8e\u8fd9\u4e2a\u53c2\u6570\u6211\u6709\u65b0\u7684\u53d1\u73b0\u4f1a\u7ee7\u7eed\u66f4\u65b0\u3002<\/li>\n<\/ul>\n<p>\u4e0a\u8ff0\u7684\u51c6\u5907\u5de5\u4f5c\u505a\u597d\u4e4b\u540e\uff0c\u6211\u4eec\u53ef\u4ee5\u76f4\u63a5\u56de\u8f66\u8fdb\u884c\u5206\u6790\u5566\uff01\u6574\u4e2a\u8fc7\u7a0b\u5927\u69828-9\u5206\u949f\u3002<br \/>\n<div class='fancybox-wrapper lazyload-container-unload' data-fancybox='post-images' href='http:\/\/www.alearnerlin.top\/wp-content\/uploads\/2024\/03\/\u5fae\u4fe1\u56fe\u7247_20240309184736.png'><img class=\"lazyload lazyload-style-1\" src=\"data:image\/svg+xml;base64,PCEtLUFyZ29uTG9hZGluZy0tPgo8c3ZnIHdpZHRoPSIxIiBoZWlnaHQ9IjEiIHhtbG5zPSJodHRwOi8vd3d3LnczLm9yZy8yMDAwL3N2ZyIgc3Ryb2tlPSIjZmZmZmZmMDAiPjxnPjwvZz4KPC9zdmc+\"  decoding=\"async\" data-original=\"http:\/\/www.alearnerlin.top\/wp-content\/uploads\/2024\/03\/\u5fae\u4fe1\u56fe\u7247_20240309184736.png\" src=\"data:image\/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAEAAAABCAYAAAAfFcSJAAAAAXNSR0IArs4c6QAAAARnQU1BAACxjwv8YQUAAAAJcEhZcwAADsQAAA7EAZUrDhsAAAANSURBVBhXYzh8+PB\/AAffA0nNPuCLAAAAAElFTkSuQmCC\" alt=\"\" \/><\/div><\/p>\n<p>\u6700\u540e\u6211\u4eec\u53ef\u4ee5\u5f97\u5230\u4e00\u4e2asmr\u540e\u7f00\u7684\u6587\u4ef6\u3002\u53ef\u4ee5\u76f4\u63a5\u4f7f\u7528excel\u6253\u5f00\uff0c\u6216\u8005\u590d\u5236\u4ee5\u540e\u66f4\u6539\u6210xls\u683c\u5f0f\u6253\u5f00\u3002<br \/>\n\u5177\u4f53\u7684\u7ed3\u679c\u5206\u6790\uff0c\u4e3b\u8981\u5173\u6ce8SMR\u7684P\u503c\uff0c\u548cHEIDI\u68c0\u9a8c\u7684P\u503c\u3002\u8be6\u7ec6\u5206\u6790\u8fc7\u7a0b\uff0c\u53ef\u4ee5\u591a\u770b\u770b\u5b98\u7f51\u63d0\u4f9b\u7684\u8bba\u6587\u3002<br \/>\n<div class='fancybox-wrapper lazyload-container-unload' data-fancybox='post-images' href='http:\/\/www.alearnerlin.top\/wp-content\/uploads\/2024\/03\/\u5fae\u4fe1\u622a\u56fe_20240309184837.jpg'><img class=\"lazyload lazyload-style-1\" src=\"data:image\/svg+xml;base64,PCEtLUFyZ29uTG9hZGluZy0tPgo8c3ZnIHdpZHRoPSIxIiBoZWlnaHQ9IjEiIHhtbG5zPSJodHRwOi8vd3d3LnczLm9yZy8yMDAwL3N2ZyIgc3Ryb2tlPSIjZmZmZmZmMDAiPjxnPjwvZz4KPC9zdmc+\"  decoding=\"async\" data-original=\"http:\/\/www.alearnerlin.top\/wp-content\/uploads\/2024\/03\/\u5fae\u4fe1\u622a\u56fe_20240309184837.jpg\" src=\"data:image\/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAEAAAABCAYAAAAfFcSJAAAAAXNSR0IArs4c6QAAAARnQU1BAACxjwv8YQUAAAAJcEhZcwAADsQAAA7EAZUrDhsAAAANSURBVBhXYzh8+PB\/AAffA0nNPuCLAAAAAElFTkSuQmCC\" alt=\"\" \/><\/div><\/p>\n<p>\u4ee5\u4e0a\u5c31\u662fSMR\u5206\u6790\u7684\u6574\u4e2a\u8fc7\u7a0b\uff0c\u9664\u6b64\u4e4b\u5916SMR\u8fd8\u6709\u53ef\u4ee5\u8fdb\u884c\u5176\u4ed6\u7684\u5206\u6790\u3002\u5e0c\u671b\u5927\u5bb6\u79ef\u6781\u63a2\u7d22\u53d1\u73b0\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"<p>SMR\u7b80\u4ecb\u4ee5\u53ca\u4ee3\u7801\u5b9e\u64cd \u4e00\u3001\u7b80\u4ecb SMR\u662f\u7531\u897f\u6e56\u5927\u5b66\u6768\u5065\u6559\u6388\u56e2\u961f\u5f00\u53d1\u5e76\u652f\u6301\u7684\u4e00\u4e2a\u8fdb\u884cSMR\u4ee5\u53caHEIDI\u68c0\u9a8c\u7684 [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[11],"tags":[],"class_list":["post-148","post","type-post","status-publish","format-standard","hentry","category-r"],"_links":{"self":[{"href":"http:\/\/www.alearnerlin.top\/index.php\/wp-json\/wp\/v2\/posts\/148","targetHints":{"allow":["GET"]}}],"collection":[{"href":"http:\/\/www.alearnerlin.top\/index.php\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.alearnerlin.top\/index.php\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.alearnerlin.top\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.alearnerlin.top\/index.php\/wp-json\/wp\/v2\/comments?post=148"}],"version-history":[{"count":12,"href":"http:\/\/www.alearnerlin.top\/index.php\/wp-json\/wp\/v2\/posts\/148\/revisions"}],"predecessor-version":[{"id":193,"href":"http:\/\/www.alearnerlin.top\/index.php\/wp-json\/wp\/v2\/posts\/148\/revisions\/193"}],"wp:attachment":[{"href":"http:\/\/www.alearnerlin.top\/index.php\/wp-json\/wp\/v2\/media?parent=148"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.alearnerlin.top\/index.php\/wp-json\/wp\/v2\/categories?post=148"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.alearnerlin.top\/index.php\/wp-json\/wp\/v2\/tags?post=148"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}