{"id":43140,"date":"2024-06-01T22:22:48","date_gmt":"2024-06-01T14:22:48","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=43140"},"modified":"2024-06-01T22:48:57","modified_gmt":"2024-06-01T14:48:57","slug":"%e6%8e%a2%e7%b4%a2%e5%ad%9f%e5%be%b7%e5%b0%94%e9%9a%8f%e6%9c%ba%e5%8c%96%e7%a0%94%e7%a9%b6%e7%9a%84%e5%88%a9%e5%99%a8%ef%bc%9atwosamplemr","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=43140","title":{"rendered":"\u63a2\u7d22\u5b5f\u5fb7\u5c14\u968f\u673a\u5316\u7814\u7a76\u7684\u5229\u5668\uff1aTwoSampleMR"},"content":{"rendered":"\n<h1 class=\"wp-block-heading\"><\/h1>\n\n\n\n<p>\u5b5f\u5fb7\u5c14\u968f\u673a\u5316\uff08Mendelian Randomization\uff0cMR\uff09\u662f\u4e00\u79cd\u5229\u7528\u57fa\u56e0\u53d8\u5f02\u4f5c\u4e3a\u5de5\u5177\u53d8\u91cf\u6765\u63a2\u8ba8\u66b4\u9732\u56e0\u7d20\u4e0e\u75be\u75c5\u4e4b\u95f4\u56e0\u679c\u5173\u7cfb\u7684\u65b9\u6cd5\u3002\u5728\u8fd9\u4e00\u9886\u57df\u4e2d\uff0cTwoSampleMR\u662f\u4e00\u4e2a\u5f3a\u5927\u4e14\u7075\u6d3b\u7684\u5de5\u5177\uff0c\u4e3a\u7814\u7a76\u4eba\u5458\u63d0\u4f9b\u4e86\u4e30\u5bcc\u7684\u529f\u80fd\u548c\u5206\u6790\u80fd\u529b\u3002\u672c\u6587\u5c06\u8be6\u7ec6\u4ecb\u7ecdTwoSampleMR\u7684\u529f\u80fd\u3001\u4f7f\u7528\u65b9\u6cd5\u53ca\u5176\u5728\u5b5f\u5fb7\u5c14\u968f\u673a\u5316\u7814\u7a76\u4e2d\u7684\u91cd\u8981\u6027\u3002<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">\u4ec0\u4e48\u662fTwoSampleMR\uff1f<\/h2>\n\n\n\n<p>TwoSampleMR\u662f\u4e00\u4e2a\u57fa\u4e8eR\u8bed\u8a00\u7684\u5305\uff0c\u8bbe\u8ba1\u7528\u4e8e\u6267\u884c\u4e24\u6837\u672c\u5b5f\u5fb7\u5c14\u968f\u673a\u5316\u5206\u6790\u3002\u8be5\u5305\u4e0eMR-Base\u7d27\u5bc6\u96c6\u6210\uff0c\u5141\u8bb8\u7528\u6237\u8f7b\u677e\u8bbf\u95ee\u548c\u5206\u6790\u5927\u89c4\u6a21\u7684\u57fa\u56e0\u7ec4\u5173\u8054\u7814\u7a76\uff08Genome-Wide Association Studies, GWAS\uff09\u6570\u636e\u3002TwoSampleMR\u7279\u522b\u9002\u5408\u9700\u8981\u9ad8\u7075\u6d3b\u6027\u548c\u53ef\u91cd\u590d\u6027\u7684\u7814\u7a76\u4eba\u5458\uff0c\u63d0\u4f9b\u4e86\u591a\u79cd\u5206\u6790\u5de5\u5177\u548c\u65b9\u6cd5\u3002<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">TwoSampleMR\u7684\u4e3b\u8981\u529f\u80fd<\/h2>\n\n\n\n<h3 class=\"wp-block-heading\">1. \u6570\u636e\u83b7\u53d6<\/h3>\n\n\n\n<p>TwoSampleMR\u63d0\u4f9b\u7b80\u5355\u7684\u63a5\u53e3\uff0c\u65b9\u4fbf\u7528\u6237\u4eceMR-Base\u83b7\u53d6GWAS\u6458\u8981\u7edf\u8ba1\u6570\u636e\u3002\u7528\u6237\u53ea\u9700\u51e0\u884c\u4ee3\u7801\u5373\u53ef\u4e0b\u8f7d\u5e76\u5bfc\u5165\u6240\u9700\u7684\u6570\u636e\uff0c\u4e3a\u540e\u7eed\u5206\u6790\u505a\u597d\u51c6\u5907\u3002<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>library(TwoSampleMR)\nexposure_data &lt;- extract_instruments(outcomes = \"ieu-a-2\")\noutcome_data &lt;- extract_outcome_data(snps = exposure_data$SNP, outcomes = \"ieu-a-7\")<\/code><\/pre>\n\n\n\n<h3 class=\"wp-block-heading\">2. \u6570\u636e\u5904\u7406<\/h3>\n\n\n\n<p>TwoSampleMR\u5305\u542b\u5f3a\u5927\u7684\u6570\u636e\u6e05\u6d17\u548c\u51c6\u5907\u5de5\u5177\uff0c\u786e\u4fdd\u6570\u636e\u7684\u4e00\u81f4\u6027\u548c\u51c6\u786e\u6027\u3002\u901a\u8fc7\u8fd9\u4e9b\u5de5\u5177\uff0c\u7528\u6237\u53ef\u4ee5\u8f7b\u677e\u5904\u7406\u7f3a\u5931\u503c\u3001\u8fdb\u884c\u6570\u636e\u6807\u51c6\u5316\uff0c\u5e76\u51c6\u5907\u597d\u7528\u4e8eMR\u5206\u6790\u7684\u6570\u636e\u96c6\u3002<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>harmonised_data &lt;- harmonise_data(exposure_data, outcome_data)<\/code><\/pre>\n\n\n\n<h3 class=\"wp-block-heading\">3. \u591a\u79cdMR\u5206\u6790\u65b9\u6cd5<\/h3>\n\n\n\n<p>TwoSampleMR\u652f\u6301\u591a\u79cdMR\u5206\u6790\u65b9\u6cd5\uff0c\u5305\u62ec\u4f46\u4e0d\u9650\u4e8e\uff1a<\/p>\n\n\n\n<ul>\n<li><strong>\u9006\u65b9\u5dee\u52a0\u6743\u6cd5\uff08Inverse Variance Weighted, IVW\uff09\uff1a<\/strong> \u6700\u5e38\u7528\u7684MR\u5206\u6790\u65b9\u6cd5\uff0c\u901a\u8fc7\u52a0\u6743\u5e73\u5747\u6765\u4f30\u8ba1\u66b4\u9732\u4e0e\u7ed3\u679c\u4e4b\u95f4\u7684\u56e0\u679c\u6548\u5e94\u3002<\/li>\n\n\n\n<li><strong>MR-Egger\u56de\u5f52\uff1a<\/strong> \u7528\u4e8e\u68c0\u6d4b\u548c\u6821\u6b63\u57fa\u56e0\u591a\u6548\u6027\u3002<\/li>\n\n\n\n<li><strong>\u52a0\u6743\u4e2d\u4f4d\u6570\u6cd5\uff08Weighted Median\uff09\uff1a<\/strong> \u63d0\u4f9b\u4e86\u4e00\u79cd\u9c81\u68d2\u7684\u56e0\u679c\u6548\u5e94\u4f30\u8ba1\u65b9\u6cd5\uff0c\u7279\u522b\u9002\u7528\u4e8e\u5b58\u5728\u5f02\u5e38\u503c\u7684\u60c5\u51b5\u3002<\/li>\n\n\n\n<li><strong>\u52a0\u6743\u6a21\u5f0f\u6cd5\uff08Weighted Mode\uff09\uff1a<\/strong> \u53e6\u4e00\u79cd\u9c81\u68d2\u7684\u4f30\u8ba1\u65b9\u6cd5\uff0c\u9002\u7528\u4e8e\u6570\u636e\u4e2d\u5b58\u5728\u591a\u6548\u6027\u7684\u60c5\u51b5\u3002<\/li>\n<\/ul>\n\n\n\n<pre class=\"wp-block-code\"><code>mr_results &lt;- mr(harmonised_data, method_list = c(\"mr_ivw\", \"mr_egger\", \"mr_weighted_median\"))<\/code><\/pre>\n\n\n\n<h3 class=\"wp-block-heading\">4. \u654f\u611f\u6027\u5206\u6790<\/h3>\n\n\n\n<p>\u4e3a\u4e86\u786e\u4fdd\u7ed3\u679c\u7684\u53ef\u9760\u6027\uff0cTwoSampleMR\u63d0\u4f9b\u591a\u79cd\u654f\u611f\u6027\u5206\u6790\u5de5\u5177\uff0c\u4ee5\u68c0\u6d4b\u548c\u6821\u6b63\u6f5c\u5728\u7684\u504f\u501a\u548c\u591a\u6548\u6027\u3002\u8fd9\u4e9b\u5de5\u5177\u5305\u62ec\u5f02\u8d28\u6027\u68c0\u9a8c\u3001\u53bb\u6781\u503c\u5206\u6790\u7b49\u3002<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>heterogeneity_test &lt;- mr_heterogeneity(harmonised_data)\npleiotropy_test &lt;- mr_pleiotropy_test(harmonised_data)<\/code><\/pre>\n\n\n\n<h3 class=\"wp-block-heading\">5. \u7ed3\u679c\u53ef\u89c6\u5316<\/h3>\n\n\n\n<p>TwoSampleMR\u5185\u7f6e\u4e86\u4e30\u5bcc\u7684\u53ef\u89c6\u5316\u5de5\u5177\uff0c\u5e2e\u52a9\u7528\u6237\u751f\u6210\u9ad8\u8d28\u91cf\u7684\u56fe\u8868\uff0c\u76f4\u89c2\u5730\u5c55\u793a\u5206\u6790\u7ed3\u679c\u3002\u8fd9\u4e9b\u56fe\u8868\u5305\u62ec\u6563\u70b9\u56fe\u3001\u68ee\u6797\u56fe\u548c\u6f0f\u6597\u56fe\u7b49\uff0c\u80fd\u591f\u6709\u6548\u5730\u5448\u73b0\u6570\u636e\u7684\u5206\u5e03\u548c\u7edf\u8ba1\u7ed3\u679c\u3002<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>mr_scatter_plot(mr_results, harmonised_data)<\/code><\/pre>\n\n\n\n<h2 class=\"wp-block-heading\">\u5982\u4f55\u4f7f\u7528TwoSampleMR\uff1f<\/h2>\n\n\n\n<h3 class=\"wp-block-heading\">\u6b65\u9aa4\u4e00\uff1a\u5b89\u88c5\u548c\u52a0\u8f7dTwoSampleMR\u5305<\/h3>\n\n\n\n<p>\u9996\u5148\uff0c\u7528\u6237\u9700\u8981\u5728R\u73af\u5883\u4e2d\u5b89\u88c5\u5e76\u52a0\u8f7dTwoSampleMR\u5305\u3002\u53ef\u4ee5\u4f7f\u7528\u4ee5\u4e0b\u547d\u4ee4\u5b89\u88c5\u8be5\u5305\uff1a<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>install.packages(\"devtools\")\ndevtools::install_github(\"MRCIEU\/TwoSampleMR\")\nlibrary(TwoSampleMR)<\/code><\/pre>\n\n\n\n<h3 class=\"wp-block-heading\">\u6b65\u9aa4\u4e8c\uff1a\u83b7\u53d6\u548c\u5904\u7406\u6570\u636e<\/h3>\n\n\n\n<p>\u63a5\u4e0b\u6765\uff0c\u7528\u6237\u53ef\u4ee5\u4f7f\u7528TwoSampleMR\u63d0\u4f9b\u7684\u63a5\u53e3\u4eceMR-Base\u83b7\u53d6GWAS\u6570\u636e\uff0c\u5e76\u8fdb\u884c\u6570\u636e\u5904\u7406\u548c\u6807\u51c6\u5316\u3002<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>exposure_data &lt;- extract_instruments(outcomes = \"ieu-a-2\")\noutcome_data &lt;- extract_outcome_data(snps = exposure_data$SNP, outcomes = \"ieu-a-7\")\nharmonised_data &lt;- harmonise_data(exposure_data, outcome_data)<\/code><\/pre>\n\n\n\n<h3 class=\"wp-block-heading\">\u6b65\u9aa4\u4e09\uff1a\u9009\u62e9\u548c\u8fd0\u884cMR\u5206\u6790\u65b9\u6cd5<\/h3>\n\n\n\n<p>\u6839\u636e\u7814\u7a76\u9700\u6c42\uff0c\u7528\u6237\u53ef\u4ee5\u9009\u62e9\u5408\u9002\u7684MR\u5206\u6790\u65b9\u6cd5\uff0c\u5e76\u8fd0\u884c\u5206\u6790\u3002<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>mr_results &lt;- mr(harmonised_data, method_list = c(\"mr_ivw\", \"mr_egger\", \"mr_weighted_median\"))<\/code><\/pre>\n\n\n\n<h3 class=\"wp-block-heading\">\u6b65\u9aa4\u56db\uff1a\u8fdb\u884c\u654f\u611f\u6027\u5206\u6790<\/h3>\n\n\n\n<p>\u4e3a\u4e86\u786e\u4fdd\u5206\u6790\u7ed3\u679c\u7684\u53ef\u9760\u6027\uff0c\u7528\u6237\u53ef\u4ee5\u8fdb\u884c\u591a\u79cd\u654f\u611f\u6027\u5206\u6790\u3002<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>heterogeneity_test &lt;- mr_heterogeneity(harmonised_data)\npleiotropy_test &lt;- mr_pleiotropy_test(harmonised_data)<\/code><\/pre>\n\n\n\n<h3 class=\"wp-block-heading\">\u6b65\u9aa4\u4e94\uff1a\u7ed3\u679c\u53ef\u89c6\u5316<\/h3>\n\n\n\n<p>\u6700\u540e\uff0c\u7528\u6237\u53ef\u4ee5\u751f\u6210\u548c\u67e5\u770b\u5206\u6790\u7ed3\u679c\u7684\u53ef\u89c6\u5316\u56fe\u8868\u3002<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>mr_scatter_plot(mr_results, harmonised_data)<\/code><\/pre>\n\n\n\n<h2 class=\"wp-block-heading\">TwoSampleMR\u7684\u4f18\u52bf<\/h2>\n\n\n\n<h3 class=\"wp-block-heading\">1. \u9ad8\u5ea6\u7075\u6d3b\u6027<\/h3>\n\n\n\n<p>TwoSampleMR\u57fa\u4e8eR\u8bed\u8a00\uff0c\u63d0\u4f9b\u4e86\u9ad8\u5ea6\u7684\u7075\u6d3b\u6027\u548c\u53ef\u5b9a\u5236\u6027\u3002\u7528\u6237\u53ef\u4ee5\u6839\u636e\u5177\u4f53\u7684\u7814\u7a76\u9700\u6c42\uff0c\u81ea\u7531\u9009\u62e9\u548c\u7ec4\u5408\u4e0d\u540c\u7684\u5206\u6790\u65b9\u6cd5\u548c\u5de5\u5177\u3002<\/p>\n\n\n\n<h3 class=\"wp-block-heading\">2. \u5f3a\u5927\u529f\u80fd<\/h3>\n\n\n\n<p>TwoSampleMR\u96c6\u6210\u4e86\u591a\u79cd\u5148\u8fdb\u7684MR\u5206\u6790\u65b9\u6cd5\u548c\u654f\u611f\u6027\u5206\u6790\u5de5\u5177\uff0c\u80fd\u591f\u6ee1\u8db3\u590d\u6742\u7684\u7814\u7a76\u9700\u6c42\u3002\u65e0\u8bba\u662f\u57fa\u672c\u7684\u56e0\u679c\u63a8\u65ad\uff0c\u8fd8\u662f\u591a\u6548\u6027\u6821\u6b63\uff0cTwoSampleMR\u90fd\u80fd\u63d0\u4f9b\u6709\u6548\u7684\u89e3\u51b3\u65b9\u6848\u3002<\/p>\n\n\n\n<h3 class=\"wp-block-heading\">3. \u6613\u4e8e\u96c6\u6210<\/h3>\n\n\n\n<p>TwoSampleMR\u4e0eMR-Base\u7d27\u5bc6\u96c6\u6210\uff0c\u7528\u6237\u53ef\u4ee5\u8f7b\u677e\u83b7\u53d6\u548c\u5229\u7528\u5927\u89c4\u6a21\u7684GWAS\u6570\u636e\u3002\u6b64\u5916\uff0cTwoSampleMR\u8fd8\u53ef\u4ee5\u4e0e\u5176\u4ed6R\u5305\u548c\u6570\u636e\u5206\u6790\u5de5\u5177\u65e0\u7f1d\u5bf9\u63a5\uff0c\u63d0\u9ad8\u4e86\u7814\u7a76\u7684\u6548\u7387\u548c\u7075\u6d3b\u6027\u3002<\/p>\n\n\n\n<h3 class=\"wp-block-heading\">4. \u793e\u533a\u652f\u6301<\/h3>\n\n\n\n<p>TwoSampleMR\u6709\u4e00\u4e2a\u6d3b\u8dc3\u7684\u7528\u6237\u793e\u533a\uff0c\u7814\u7a76\u4eba\u5458\u53ef\u4ee5\u5728\u793e\u533a\u4e2d\u5206\u4eab\u7ecf\u9a8c\u3001\u4ea4\u6d41\u95ee\u9898\uff0c\u5e76\u83b7\u53d6\u6280\u672f\u652f\u6301\u3002\u8fd9\u79cd\u5f00\u653e\u548c\u534f\u4f5c\u7684\u7814\u7a76\u73af\u5883\uff0c\u6709\u52a9\u4e8e\u63a8\u52a8\u5b5f\u5fb7\u5c14\u968f\u673a\u5316\u7814\u7a76\u7684\u8fdb\u6b65\u3002<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">\u7ed3\u8bed<\/h2>\n\n\n\n<p>TwoSampleMR\u4f5c\u4e3a\u5b5f\u5fb7\u5c14\u968f\u673a\u5316\u7814\u7a76\u4e2d\u7684\u91cd\u8981\u5de5\u5177\uff0c\u4e3a\u7814\u7a76\u4eba\u5458\u63d0\u4f9b\u4e86\u4e30\u5bcc\u7684\u529f\u80fd\u548c\u5206\u6790\u80fd\u529b\u3002\u901a\u8fc7TwoSampleMR\uff0c\u7528\u6237\u53ef\u4ee5\u8f7b\u677e\u83b7\u53d6\u548c\u5206\u6790\u5927\u89c4\u6a21\u7684GWAS\u6570\u636e\uff0c\u8fdb\u884c\u9ad8\u8d28\u91cf\u7684MR\u7814\u7a76\u3002\u672a\u6765\uff0c\u968f\u7740TwoSampleMR\u7684\u4e0d\u65ad\u53d1\u5c55\u548c\u5b8c\u5584\uff0c\u5fc5\u5c06\u4e3a\u5b5f\u5fb7\u5c14\u968f\u673a\u5316\u7814\u7a76\u5e26\u6765\u66f4\u591a\u521b\u65b0\u548c\u7a81\u7834\uff0c\u63a8\u52a8\u9057\u4f20\u6d41\u884c\u75c5\u5b66\u9886\u57df\u7684\u53d1\u5c55\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u5b5f\u5fb7\u5c14\u968f\u673a\u5316\uff08Mendelian Randomization\uff0cMR\uff09\u662f\u4e00\u79cd\u5229\u7528\u57fa\u56e0\u53d8\u5f02\u4f5c\u4e3a\u5de5\u5177\u53d8\u91cf\u6765\u63a2\u8ba8\u66b4\u9732\u56e0 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