{"id":25077,"date":"2024-01-18T16:41:44","date_gmt":"2024-01-18T08:41:44","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=25077"},"modified":"2024-01-18T16:41:45","modified_gmt":"2024-01-18T08:41:45","slug":"%e7%94%9f%e4%bf%a1%e5%bf%85%e5%a4%87%e5%88%86%e6%9e%90%e5%86%85%e5%ae%b9%ef%bc%8ccox%e6%a8%a1%e5%9e%8b%e8%af%84%e4%bc%b0-%e5%86%b3%e7%ad%96%e6%9b%b2%e7%ba%bf%e5%88%86%e6%9e%90%ef%bc%88dca%ef%bc%89","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=25077","title":{"rendered":"\u751f\u4fe1\u5fc5\u5907\u5206\u6790\u5185\u5bb9\uff0ccox\u6a21\u578b\u8bc4\u4f30-\u51b3\u7b56\u66f2\u7ebf\u5206\u6790\uff08DCA\uff09"},"content":{"rendered":"

\u4eca\u5929\u5c0f\u679c\u4e3a\u5c0f\u4f19\u4f34\u4eec\u5e26\u6765\u7684\u5206\u4eab\u4e3a\u5229\u7528DCA\u5206\u6790\u8bc4\u4ef7\u6a21\u578b\u7684\u4e34\u5e8a\u51c0\u83b7\u76ca\u7387\uff0c\u8be5\u5206\u6790\u5728\u6a21\u578b\u8bc4\u4ef7\u4e2d\u662f\u7f3a\u4e00\u4e0d\u53ef\u7684\u5206\u6790\uff0c\u5c0f\u679c\u5c06\u901a\u8fc7\u8be5\u63a8\u6587\u4ecb\u7ecd\u5982\u4f55\u8fdb\u884c\u6a21\u578b\u8bc4\u4ef7\u548c\u6a21\u578b\u4e2d\u6307\u6807\u7684\u4e34\u5e8a\u51c0\u83b7\u76ca\u7387\uff0c\u8be5\u5206\u6790\u975e\u5e38\u503c\u5f97\u5c0f\u4f19\u4f34\u5b66\u4e60\uff0c\u5c0f\u679c\u5f3a\u70c8\u63a8\u8350\uff0c\u63a5\u4e0b\u6765\u548c\u5c0f\u679c\u4e00\u8d77\u5f00\u59cb\u4eca\u5929\u7684\u5b66\u4e60\u5427\uff01<\/p>\n

1.\u4f55\u4e3aDCA\u5206\u6790\uff1f<\/p>\n

\u5728\u5f00\u59cb\u8be5\u5206\u6790\u4e4b\u524d\uff0c\u5c0f\u679c\u5148\u4e3a\u5c0f\u4f19\u4f34\u4eec\u7b80\u5355\u4ecb\u7ecd\u4e00\u4e0b\u4f55\u4e3aDCA\u5206\u6790\uff1fDCA\u66f2\u7ebf\uff0c\u5373\u51b3\u7b56\u66f2\u7ebf\u5206\u6790\u6cd5\uff08Decision Curve Analysis\uff09,\u662f\u7528\u6765\u5e2e\u52a9\u786e\u5b9a\u9ad8\u98ce\u9669\u60a3\u8005\u8fdb\u884c\u5e72\u9884\uff0c\u800c\u4f4e\u98ce\u9669\u60a3\u8005\u907f\u514d\u5e72\u9884\uff08\u907f\u514d\u8fc7\u5ea6\u533b\u7597\uff09\uff0c\u5373\u8bc4\u4ef7\u60a3\u8005\u83b7\u76ca\u7a0b\u5ea6\u7684\u4e00\u79cd\u8bc4\u4f30\u65b9\u6cd5\u3002\u8fd9\u5c31\u662f\u5c0f\u679c\u5bf9DCA\u5206\u6790\u7684\u7b80\u5355\u4ecb\u7ecd\uff0c\u5c0f\u4f19\u4f34\u4eec\u662f\u4e0d\u662f\u5f88\u5bb9\u6613\u7406\u89e3\u5440\uff01\u6709\u4e0d\u7406\u89e3\u7684\u5c0f\u4f19\u4f34\uff0c\u53ef\u4ee5\u81ea\u884c\u5230\u7f51\u4e0a\u67e5\u8be2\u6df1\u5165\u5b66\u4e60\u5440\uff01\u9a6c\u4e0a\u548c\u5c0f\u679c\u4e00\u8d77\u5f00\u542f\u4eca\u5929\u7684\u5b9e\u64cd\u3002<\/p>\n

2.\u51c6\u5907\u9700\u8981\u7684R\u5305<\/p>\n

#\u5b89\u88c5\u9700\u8981\u7684R\u5305<\/p>\n

install.packages(“survival”)<\/p>\n

#\u52a0\u8f7d\u9700\u8981\u7684R\u5305<\/p>\n

library(survival)<\/p>\n

library(ggDCA)<\/p>\n

library(tidyverse)<\/p>\n

source(“stdca.R”)<\/p>\n

3.\u8bfb\u53d6\u8f93\u5165\u6570\u636e<\/p>\n

#\u884c\u540d\u4e3a\u6837\u672c\u540d\uff0c\u5176\u4ed6\u5217\u4e3a\u4e34\u5e8a\u56e0\u7d20\uff0c\u4e3b\u8981\u5305\u62ec\u751f\u5b58\u65f6\u95f4\uff0c\u751f\u5b58\u72b6\u6001\u7b49\u4fe1\u606f\u3002<\/p>\n

pbc<-read.table(“easy_input.txt”)<\/p>\n

\"Dingtalk_20230706152222\"<\/p>\n

#\u5220\u6389\u7f3a\u5931\u6570\u636e<\/p>\n

pbc <- na.omit(pbc)<\/p>\n

#\u5148\u628abili\u5206\u4e3a\u4e09\u7c7b\uff1a\u4f4e\u3001\u4e2d\u3001\u9ad8<\/p>\n

pbc$catbili <- cut(pbc$bili,breaks=c(-Inf, 2, 4, Inf),<\/p>\n

labels=c(“low”,”medium”,”high”))<\/p>\n

#\u628astatus\u5206\u4e3a\u4e24\u7c7b\uff0c\u539f\u6765\u76842\u4e3a\u53d8\u62101\uff0c\u539f\u6765\u76841\u548c0\u53d8\u62100<\/p>\n

pbc$died <- pbc$status==2<\/p>\n

pbc$status =ifelse(pbc$died==”TRUE”,1,0)<\/p>\n

    \n
  1. DCA\u5206\u6790\u8bc4\u4ef7\u6a21\u578b\u7684\u4e34\u5e8a\u51c0\u83b7\u76ca\u7387<\/li>\n<\/ol>\n

    #\u591a\u56e0\u7d20\u56de\u5f52\u5206\u6790<\/p>\n

    Srv = Surv(pbc$time, pbc$died)<\/p>\n

    #\u6b64\u5904\u9009\u62e95\u5e74\u7684\u65f6\u95f4\u8282\u70b9\uff0c\u8f93\u5165\u6587\u4ef6\u7684time\u5217\u7684\u5355\u4f4d\u662f\u5929\uff0c5\u5e74\u662f1825\u5929\u3002<\/p>\n

    #\u4e0b\u9762\u6bcf\u4e24\u884c\u8ba1\u7b971\u79cdcox\u6a21\u578b\u7684\u7cfb\u6570\uff0c\u540e\u9762\u5c06\u753b\u56fe\u5bf9\u6bd4<\/p>\n

    #\u6a21\u578b\u4e00<\/p>\n

    coxmod1 = coxph(Srv ~ trt + age + sex + hepato + catbili + copper + stage, data=pbc)<\/p>\n

    pbc$model1 = c(1 – (summary(survfit(coxmod1,newdata=pbc), times=1825)$surv))<\/p>\n

    #\u6a21\u578b\u4e8c<\/p>\n

    coxmod2 = coxph(Srv ~ ascites + spiders + edema + chol + albumin + alk.phos + ast + trig + platelet + protime, data=pbc)<\/p>\n

    pbc$model2 = c(1 – (summary(survfit(coxmod2,newdata=pbc), times=1825)$surv))<\/p>\n

    #\u6a21\u578b\u4e09<\/p>\n

    coxmod3 = coxph(Srv ~ trt + age + sex + hepato + catbili + copper + stage + ascites + spiders + edema + chol + albumin + alk.phos + ast + trig + platelet + protime, data=pbc)<\/p>\n

    pbc$model3 = c(1 – (summary(survfit(coxmod3,newdata=pbc), times=1825)$surv))<\/p>\n

    #\u6a21\u578b\u56db<\/p>\n

    coxmod4 = coxph(Srv ~ stage, data=pbc)<\/p>\n

    pbc$model4 = c(1 – (summary(survfit(coxmod4,newdata=pbc), times=1825)$surv))<\/p>\n

    \"Dingtalk_20230706160114\"<\/p>\n

    #\u753b\u4e00\u6761\u4e34\u5e8a\u51c0\u83b7\u76ca\u7387<\/p>\n

    mod1<-stdca(data=pbc, outcome=”status”, ttoutcome=”time”, timepoint=1825,<\/p>\n

    predictors=”model1″,cmprsk=TRUE,smooth=TRUE, xstop=0.5,intervention=”FALSE”)<\/p>\n

    \"Dingtalk_20230706161755\"<\/p>\n

    #\u591a\u4e2a\u6a21\u578b\u6bd4\u8f83<\/p>\n

    pdf(“net_benefit.pdf”,width = 6,height = 6)<\/p>\n

    stdca(data=pbc, outcome=”status”, ttoutcome=”time”, timepoint=1825,<\/p>\n

    predictors=c(“model1″,”model2″,”model3″,”model4″),<\/p>\n

    cmprsk=TRUE, smooth=TRUE,<\/p>\n

    xstop=0.5,intervention=”FALSE”)<\/p>\n

    dev.off()<\/p>\n

    \"Dingtalk_20230706162213\"<\/p>\n

      \n
    1. DCA\u5206\u6790\u8bc4\u4ef7\u6a21\u578b\u7684\u5e72\u9884\u4e34\u5e8a\u51c0\u83b7\u76ca\u7387<\/li>\n<\/ol>\n

      #\u753b\u4e00\u6761\u5e72\u9884\u4e34\u5e8a\u51c0\u83b7\u76ca\u7387<\/p>\n

      pdf(“3red.pdf”)<\/p>\n

      mod1 <- stdca(data=pbc, outcome=”status”, ttoutcome=”time”, timepoint=1825,<\/p>\n

      predictors=”model1″,cmprsk=TRUE,smooth=TRUE, xstop=0.5,intervention=”TRUE”)<\/p>\n

      dev.off()<\/p>\n

      \"Dingtalk_20230706162827\"<\/p>\n

      #\u591a\u6761\u6bd4\u5bf9<\/p>\n

      pdf(“net_reduction.pdf”,width = 6,height = 6)<\/p>\n

      stdca(data=pbc, outcome=”status”, ttoutcome=”time”, timepoint=1825,<\/p>\n

      predictors=c(“model1″,”model2″,”model3″,”model4″),<\/p>\n

      cmprsk=TRUE, smooth=TRUE,<\/p>\n

      xstop=0.5,intervention=”TRUE”)<\/p>\n

      \"Dingtalk_20230706163804\"<\/p>\n

        \n
      1. ggDCA\u5305\u7ed8\u5236DCA\u66f2\u7ebf<\/li>\n<\/ol>\n

        #\u6784\u5efa\u4e24\u4e2a\u6a21\u578b<\/p>\n

        fit1 <- coxph(Surv(time,status)~age,data = pbc)<\/p>\n

        fit2 <- coxph(Surv(time,status)~trt + age + sex + hepato + catbili + copper + stage,data = pbc)<\/p>\n

        #\u7ed8\u5236\u5355\u4e2a\u6a21\u578b\u7684DCA\u66f2\u7ebf<\/p>\n

        plot1 <- dca(fit1,times = 365)<\/p>\n

        ggplot(plot1)<\/p>\n

        ggsave(“dca1.pdf”)<\/p>\n

        \"Dingtalk_20230707100321\"<\/p>\n

        #\u7ed8\u5236\u4e24\u4e2a\u6a21\u578b\u7684DCA\u66f2\u7ebf<\/p>\n

        plot2 <- dca(fit1,fit2,times = 365)<\/p>\n

        ggplot(plot2)<\/p>\n

        ggsave(“dca2.pdf”)<\/p>\n

        \"Dingtalk_20230707100457\"<\/p>\n

        \u4eca\u5929\u5c0f\u679c\u5b8c\u6210\u4e86DCA\u5206\u6790\u8bc4\u4ef7\u6a21\u578b\u7684\u4e34\u5e8a\u51c0\u83b7\u76ca\u7387\uff0c\u5176\u4ed6\u76f8\u5173\u5206\u6790\u5185\u5bb9\u6b22\u8fce\u5c1d\u8bd5\u672c\u516c\u53f8\u65b0\u5f00\u53d1\u7684\u4e91\u5e73\u53f0\u751f\u7269\u4fe1\u606f\u5206\u6790\u5c0f\u5de5\u5177\uff0c\u96f6\u4ee3\u7801\u5b8c\u6210\u5206\u6790\uff0c\u4e91\u5e73\u53f0\u7f51\u5740\uff1ahttp:\/\/www.biocloudservice.com\/home.html\uff0c\u4e3b\u8981\u5305\u62ec\u57fa\u4e8eImmuneSubtypeClassifier\u8fdb\u884c\u80bf\u7624\u514d\u75ab\u4e9a\u578b\u5206\u7c7bhttp:\/\/www.biocloudservice.com\/125\/125.php),\u4e34\u5e8a\u4e9a\u7ec4\u751f\u5b58\u5206\u6790http:\/\/www.biocloudservice.com\/386\/386.php),((lasso\u56de\u5f52\u6a21\u578b\u7b5b\u9009\u7279\u5f81\u57fa\u56e0(http:\/\/www.biocloudservice.com\/116\/116.php),\u968f\u673a\u68ee\u6797\u7684\u5341\u6298\u4ea4\u53c9\u9a8c\u8bc1(http:\/\/www.biocloudservice.com\/646\/646.php),svm-ref\u652f\u6301\u5411\u91cf\u673a\u7684\u673a\u5668\u5b66\u4e60(http:\/\/www.biocloudservice.com\/372\/372.php)\u7b49\u673a\u5668\u5b66\u4e60\u76f8\u5173\u7684\u5c0f\u5de5\u5177\uff0c\u4eca\u5929\u5c0f\u679c\u7684\u5206\u4eab\u5c31\u5230\u8fd9\u91cc\uff0c\u6b22\u8fce\u5927\u5bb6\u548c\u5c0f\u679c\u4e00\u8d77\u8ba8\u8bba\u5b66\u4e60\uff0c\u4e0b\u671f\u518d\u89c1\u5965\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"

        \u4eca\u5929\u5c0f\u679c\u4e3a\u5c0f\u4f19\u4f34\u4eec\u5e26\u6765\u7684\u5206\u4eab\u4e3a\u5229\u7528DCA\u5206\u6790\u8bc4\u4ef7\u6a21\u578b\u7684\u4e34\u5e8a\u51c0\u83b7\u76ca\u7387\uff0c\u8be5\u5206\u6790\u5728\u6a21\u578b\u8bc4\u4ef7\u4e2d\u662f\u7f3a\u4e00\u4e0d\u53ef\u7684\u5206\u6790\uff0c\u5c0f\u679c\u5c06 […]<\/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],"tags":[],"jetpack_featured_media_url":"","_links":{"self":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/25077"}],"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=25077"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/25077\/revisions"}],"predecessor-version":[{"id":25086,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/25077\/revisions\/25086"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=25077"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=25077"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=25077"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}