{"id":29063,"date":"2024-02-20T17:53:49","date_gmt":"2024-02-20T09:53:49","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=29063"},"modified":"2024-06-01T22:48:10","modified_gmt":"2024-06-01T14:48:10","slug":"%e4%b8%8d%e5%81%9a%e5%ae%9e%e9%aa%8c%e5%b0%b1%e5%8f%af%e4%bb%a5%e5%8f%91%e6%96%87%e7%ab%a0%ef%bc%8c%e4%b8%ba%e5%b0%8f%e4%bc%99%e4%bc%b4%e4%bb%ac%e5%ae%89%e5%88%a9%e5%ad%9f%e5%be%b7%e5%b0%94%e9%9a%8f","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=29063","title":{"rendered":"\u4e0d\u505a\u5b9e\u9a8c\u5c31\u53ef\u4ee5\u53d1\u6587\u7ae0\uff0c\u4e3a\u5c0f\u4f19\u4f34\u4eec\u5b89\u5229\u5b5f\u5fb7\u5c14\u968f\u673a\u5316\u5206\u6790(MR)"},"content":{"rendered":"

\u4eca\u5929\u5c0f\u679c\u4e3a\u5927\u5bb6\u5206\u4eab\u4e00\u4e0b\u4e24\u6837\u672c\u5b5f\u5fb7\u5c14\u968f\u673a\u5316\u5206\u6790\u6d41\u7a0b\uff0c\u6574\u4e2a\u5206\u6790\u8fc7\u7a0b\u6bd4\u8f83\u7b80\u5355\uff0c\u8be5\u5206\u6790\u6700\u91cd\u8981\u7684\u662f\u66b4\u9732\u56e0\u7d20\u548c\u7ed3\u5c40\u53d8\u91cfGWAS\u6570\u636e\u7684\u67e5\u627e\uff0c\u4e00\u822c\u90fd\u901a\u8fc7\u4e24\u79cd\u65b9\u5f0f\u83b7\u5f97\uff0c\u516c\u5171\u6570\u636e\u5e93\u548c\u53d1\u8868\u7684\u76f8\u5173\u6587\u7ae0\u83b7\u53d6\uff0c\u63a5\u4e0b\u6765\u5c31\u4e3a\u5927\u5bb6\u7528\u793a\u4f8b\u6570\u636e\u505a\u4e0b\u6f14\u793a\uff0c\u4ee3\u7801\u5982\u4e0b\uff1a<\/p>\n

    \n
  1. \u5b89\u88c5\u9700\u8981\u7684R\u5305<\/li>\n<\/ol>\n

    install.packages(“devtools”)<\/p>\n

    devtools::install_github(“MRCIEU\/TwoSampleMR”)<\/p>\n

    Install.packages(\u201cggplot2\u201d)<\/p>\n

      \n
    1. \u5bfc\u5165\u9700\u8981\u7684R\u5305<\/li>\n<\/ol>\n

      library(TwoSampleMR)<\/p>\n

      library(ggplot2)<\/p>\n

        \n
      1. \u5206\u6790\u8fc7\u7a0b<\/li>\n<\/ol>\n

        bmi_exp <- extract_instruments(<\/p>\n

        outcomes=ieu-a-835,<\/p>\n

        clump=TRUE, r2=0.01,<\/p>\n

        kb=5000,access_token = NULL<\/p>\n

        )<\/p>\n

        ##\u83b7\u53d6\u7ed3\u5c40\u53d8\u91cf\u6570\u636e<\/p>\n

        t2d_out <- extract_outcome_data(<\/p>\n

        snps=bmi_exp$SNP,<\/p>\n

        outcomes=ieu-a-26,<\/p>\n

        proxies = FALSE,<\/p>\n

        maf_threshold = 0.01,<\/p>\n

        access_token = NULL<\/p>\n

        )<\/p>\n

        #\u5bf9\u6570\u636e\u8fdb\u884c\u9884\u5904\u7406<\/p>\n

        mydata <- harmonise_data(<\/p>\n

        exposure_dat=bmi_exp,<\/p>\n

        outcome_dat=t2d_out,<\/p>\n

        action= 2<\/p>\n

        )<\/p>\n

        #MR\u5206\u6790<\/p>\n

        res <- mr(mydata)<\/p>\n

        write.table(res,file=”twosampleMR.txt”,sep=”\\t”,quote=F)<\/p>\n

        \"Dingtalk_20230310172212\"<\/p>\n

        ##\u654f\u611f\u6027\u5206\u6790<\/p>\n

        #\u5f02\u8d28\u6027\u68c0\u9a8c<\/p>\n

        het <- mr_heterogeneity(mydata)<\/p>\n

        het<\/p>\n

        write.table(het,file=”het.txt”,col.names=T,row.names=F,sep=”\\t”,quote=F)<\/p>\n

        #mr(mydata,method_list=c(‘mr_ivw_mre’)) #\u4f7f\u7528\u968f\u673a\u6548\u5e94\u6a21\u578b<\/p>\n

        #\u591a\u6548\u6027\u68c0\u9a8c<\/p>\n

        pleio <- mr_pleiotropy_test(mydata)<\/p>\n

        pleio<\/p>\n

        write.table(pleio,file=”pleio.txt”,col.names=T,row.names=F,sep=”\\t”,quote=F)<\/p>\n

        #\u9010\u4e2a\u5254\u9664\u68c0\u9a8c<\/p>\n

        single <- mr_leaveoneout(mydata)<\/p>\n

        #pdf(file=”leaveoneout.pdf”)<\/p>\n

        mr_leaveoneout_plot(single)<\/p>\n

        ggsave(“leaveoneout.pdf”)<\/p>\n

        \"Dingtalk_20230310171516\"<\/p>\n

        ##\u53ef\u89c6\u5316\u5206\u6790<\/p>\n

        #\u7ed8\u5236\u6563\u70b9\u56fe<\/p>\n

        mr_scatter_plot(res,mydata)<\/p>\n

        ggsave(“scatter_plot.pdf”)<\/p>\n

        \"Dingtalk_20230310171653\"<\/p>\n

        #\u7ed8\u5236\u68ee\u6797\u56fe<\/p>\n

        res_single <- mr_singlesnp(mydata)<\/p>\n

        mr_forest_plot(res_single)<\/p>\n

        ggsave(“forest_plot.pdf”)<\/p>\n

        \"Dingtalk_20230310171946\"<\/p>\n

        #\u7ed8\u5236\u6f0f\u6597\u56fe<\/p>\n

        mr_funnel_plot(res_single)<\/p>\n

        ggsave(“funnel_plot.pdf”)<\/p>\n

        \"Dingtalk_20230310172051\"<\/p>\n

        \u5c0f\u679c\u4eca\u5929\u5bf9\u4e24\u6837\u672c\u5b5f\u5fb7\u5c14\u968f\u673a\u5316\u7684\u5206\u4eab\u5c31\u5230\u8fd9\u91cc\uff0c\u6709\u9700\u8981\u7684\u53ef\u4ee5\u501f\u9274\u5b66\u4e60\u5965\uff0c\u4e0d\u8981\u5fd8\u8bb0\u70b9\u8d5e\u5173\u6ce8\u5440\uff0c\u4e0b\u671f\u5728\u89c1\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"

        \u4eca\u5929\u5c0f\u679c\u4e3a\u5927\u5bb6\u5206\u4eab\u4e00\u4e0b\u4e24\u6837\u672c\u5b5f\u5fb7\u5c14\u968f\u673a\u5316\u5206\u6790\u6d41\u7a0b\uff0c\u6574\u4e2a\u5206\u6790\u8fc7\u7a0b\u6bd4\u8f83\u7b80\u5355\uff0c\u8be5\u5206\u6790\u6700\u91cd\u8981\u7684\u662f\u66b4\u9732\u56e0\u7d20\u548c\u7ed3\u5c40\u53d8\u91cfGW […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":""},"categories":[1,64],"tags":[],"jetpack_featured_media_url":"","_links":{"self":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/29063"}],"collection":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=29063"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/29063\/revisions"}],"predecessor-version":[{"id":29069,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/29063\/revisions\/29069"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=29063"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=29063"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=29063"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}