{"id":59757,"date":"2024-06-17T08:43:58","date_gmt":"2024-06-17T00:43:58","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=59757"},"modified":"2024-06-17T08:43:58","modified_gmt":"2024-06-17T00:43:58","slug":"%e6%9e%9c%e5%ad%90%e5%b8%a6%e4%bd%a0%e6%8f%ad%e7%a4%ba%e5%9f%ba%e5%9b%a0%e4%b8%8e%e4%b8%b4%e5%ba%8a%e6%95%b0%e6%8d%ae%e9%a2%84%e6%b5%8b%e7%94%9f%e5%ad%98%e9%a2%84%e5%90%8e%e7%9a%84%e5%85%b3%e9%94%ae","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=59757","title":{"rendered":"\u679c\u5b50\u5e26\u4f60\u63ed\u793a\u57fa\u56e0\u4e0e\u4e34\u5e8a\u6570\u636e\u9884\u6d4b\u751f\u5b58\u9884\u540e\u7684\u5173\u952e\u79d8\u5bc6"},"content":{"rendered":"


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code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"cs\"><code><span class=\"code-snippet_outer\">#install.packages('survival')<\/span><\/code><code><span class=\"code-snippet_outer\">library(survival) #\u5f15\u7528\u5305<\/span><\/code><code><span class=\"code-snippet_outer\">############\u5b9a\u4e49\u68ee\u6797\u56fe\u51fd\u6570############<\/span><\/code><code><span class=\"code-snippet_outer\">#\u5b9a\u4e49\u4e86\u4e00\u4e2a\u540d\u4e3abioForest\u7684\u51fd\u6570\uff0c<\/span><\/code><code><span class=\"code-snippet_outer\">#\u8be5\u51fd\u6570\u6709\u4e09\u4e2a\u53c2\u6570\uff1acoxFile\u3001forestFile\u548cforestCol\uff0c\u8fd9\u4e9b\u53c2\u6570\u53ef\u4ee5\u5728\u51fd\u6570\u88ab\u8c03\u7528\u65f6\u4f20\u9012\u5b9e\u9645\u503c\u3002<\/span><\/code><code><span class=\"code-snippet_outer\">bioForest=function(coxFile=null, forestFile=null, forestCol=null){<\/span><\/code><code><span class=\"code-snippet_outer\"> #\u8bfb\u53d6\u8f93\u5165\u6587\u4ef6<\/span><\/code><code><span class=\"code-snippet_outer\"> rt <- read.table(coxFile, header=T, sep=\"t\", check.names=F, row.names=1)<\/span><\/code><code><span class=\"code-snippet_outer\"> #\u7528read.table\u51fd\u6570\u4ececoxFile\u4e2d\u8bfb\u53d6\u6570\u636e\uff0c\u6570\u636e\u4ee5Tab\u5206\u9694\uff0c\u5305\u542b\u8868\u5934\uff08header=T\uff09\uff0c<\/span><\/code><code><span class=\"code-snippet_outer\"> #\u7b2c\u4e00\u5217\u4f5c\u4e3a\u884c\u540d\uff08row.names=1\uff09\uff0c\u5e76\u5c06\u6570\u636e\u4fdd\u5b58\u5230\u540d\u4e3art\u7684\u6570\u636e\u6846\u4e2d\u3002<\/span><\/code><code><span class=\"code-snippet_outer\"> gene <- rownames(rt)<\/span><\/code><code><span class=\"code-snippet_outer\"> #\u5c06rt\u4e2d\u7684\u884c\u540d\uff08\u57fa\u56e0\u540d\u79f0\uff09\u4fdd\u5b58\u5230gene\u53d8\u91cf\u4e2d\u3002<\/span><\/code><code><span class=\"code-snippet_outer\"> hr <- sprintf(\"%.3f\",rt$\"HR\")<\/span><\/code><code><span class=\"code-snippet_outer\"> #\u5c06rt\u6570\u636e\u6846\u4e2d\"HR\"\u5217\u7684\u503c\u4fdd\u7559\u4e09\u4f4d\u5c0f\u6570\u5e76\u4fdd\u5b58\u5230hr\u53d8\u91cf\u4e2d\u3002<\/span><\/code><code><span class=\"code-snippet_outer\"> hrLow <- sprintf(\"%.3f\",rt$\"HR.95L\")<\/span><\/code><code><span class=\"code-snippet_outer\"> hrHigh <- sprintf(\"%.3f\",rt$\"HR.95H\")<\/span><\/code><code><span class=\"code-snippet_outer\"> Hazard.ratio <- paste0(hr,\"(\",hrLow,\"-\",hrHigh,\")\")<\/span><\/code><code><span class=\"code-snippet_outer\"> #\u4f7f\u7528paste0\u51fd\u6570\u5c06\"HR\"\u3001\"HR.95L\"\u548c\"HR.95H\"\u5217\u7684\u503c\u5408\u5e76\u4e3a\u4e00\u4e2a\u5b57\u7b26\u4e32\uff0c<\/span><\/code><code><span class=\"code-snippet_outer\"> #\u5f62\u6210\u98ce\u9669\u6bd4\u548c\u7f6e\u4fe1\u533a\u95f4\u7684\u8868\u793a\uff0c\u4fdd\u5b58\u5230Hazard.ratio\u53d8\u91cf\u4e2d\u3002<\/span><\/code><code><span class=\"code-snippet_outer\"> pVal <- ifelse(rt$pvalue<0.001, \"<0.001\", sprintf(\"%.3f\", rt$pvalue))<\/span><\/code><code><span class=\"code-snippet_outer\"> #\u7528ifelse\u51fd\u6570\uff0c\u5982\u679crt\u6570\u636e\u6846\u4e2d\u7684\"pvalue\"\u5217\u5c0f\u4e8e0.001\uff0c<\/span><\/code><code><span class=\"code-snippet_outer\"> #\u5219\u5c06pVal\u53d8\u91cf\u8bbe\u7f6e\u4e3a\"<0.001\"\uff0c\u5426\u5219\u5c06\u5176\u8bbe\u7f6e\u4e3a\u4fdd\u7559\u4e09\u4f4d\u5c0f\u6570\u7684\u5b57\u7b26\u4e32\u8868\u793a\u3002<\/span><\/code><code><span class=\"code-snippet_outer\"> #\u8f93\u51fa\u56fe\u5f62pdf\u51fd\u6570\u521b\u5efa\u4e00\u4e2a\u65b0\u7684PDF\u7ed8\u56fe\u8bbe\u5907\uff0c\u6307\u5b9a\u8f93\u51fa\u6587\u4ef6\u540d\u4e3aforestFile<\/span><\/code><code><span class=\"code-snippet_outer\"> pdf(file=forestFile, width=6.5, height=4.5)<\/span><\/code><code><span class=\"code-snippet_outer\"> n <- nrow(rt)<\/span><\/code><code><span class=\"code-snippet_outer\"> nRow <- n+1<\/span><\/code><code><span class=\"code-snippet_outer\"> ylim <- c(1,nRow)<\/span><\/code><code><span class=\"code-snippet_outer\"> layout(matrix(c(1,2),nc=2),width=c(3,2.5))<\/span><\/code><code><span class=\"code-snippet_outer\"> #\u8ba1\u7b97\u7ed8\u5236\u56fe\u5f62\u6240\u9700\u7684\u603b\u884c\u6570\uff0c\u5305\u62ec\u57fa\u56e0\u548c\u6bcf\u4e2a\u57fa\u56e0\u5bf9\u5e94\u7684\u6570\u636e\u884c\u3002\u8bbe\u7f6ey\u8f74\u7684\u8303\u56f4\uff0c\u4ece1\u5230nRow\u3002<\/span><\/code><code><span class=\"code-snippet_outer\"> #\u4f7f\u7528layout\u51fd\u6570\u8bbe\u7f6e\u7ed8\u56fe\u7684\u5e03\u5c40\uff0c\u5c06\u7ed8\u5236\u5206\u4e3a\u4e24\u5217\uff0c\u7b2c\u4e00\u5217\u5bbd\u5ea6\u4e3a3\u82f1\u5bf8\uff0c\u7b2c\u4e8c\u5217\u5bbd\u5ea6\u4e3a2.5\u82f1\u5bf8\u3002<\/span><\/code><code><span class=\"code-snippet_outer\"> #\u7ed8\u5236\u68ee\u6797\u56fe\u5de6\u8fb9\u7684\u4e34\u5e8a\u4fe1\u606f<\/span><\/code><code><span class=\"code-snippet_outer\"> xlim = c(0,3)<\/span><\/code><code><span class=\"code-snippet_outer\"> par(mar=c(4,2.5,2,1))<\/span><\/code><code><span class=\"code-snippet_outer\"> #\u7528par\u51fd\u6570\u8bbe\u7f6e\u56fe\u5f62\u7684\u7ed8\u56fe\u53c2\u6570\u3002mar\u53c2\u6570\u7528\u4e8e\u8bbe\u7f6e\u8fb9\u7f18\u7a7a\u767d\u7684\u5927\u5c0f\uff0c\u5305\u542b4\u4e2a\u503c\uff0c\u4f9d\u6b21\u4e3a\u4e0b\u3001\u5de6\u3001\u4e0a\u3001\u53f3\u7684\u8fb9\u7f18\u7a7a\u767d\u5927\u5c0f\u3002<\/span><\/code><code><span class=\"code-snippet_outer\"> plot(1,xlim=xlim,ylim=ylim,type=\"n\",axes=F,xlab=\"\",ylab=\"\")<\/span><\/code><code><span class=\"code-snippet_outer\"> text.cex=0.8<\/span><\/code><code><span class=\"code-snippet_outer\"> text(0,n:1,gene,adj=0,cex=text.cex)<\/span><\/code><code><span class=\"code-snippet_outer\"> text(1.5-0.5*0.2,n:1,pVal,adj=1,cex=text.cex);text(1.5-0.5*0.2,n+1,'pvalue',cex=text.cex,font=2,adj=1)<\/span><\/code><code><span class=\"code-snippet_outer\"> text(3.1,n:1,Hazard.ratio,adj=1,cex=text.cex);text(3.1,n+1,'Hazard ratio',cex=text.cex,font=2,adj=1)<\/span><\/code><code><span class=\"code-snippet_outer\"> #\u56fe\u4e2d\u7684\u5750\u6807(1.5-0.50.2, n:1)\u5904\u6dfb\u52a0p-value\u7684\u503c\uff0c\u5e76\u901a\u8fc7adj=1\u53c2\u6570\u5c06\u6587\u672c\u53f3\u5bf9\u9f50\uff0ccex=text.cex\u8bbe\u7f6e\u5b57\u4f53\u7f29\u653e\u3002<\/span><\/code><code><span class=\"code-snippet_outer\"> #\u7136\u540e\u5728\u5750\u6807(1.5-0.50.2, n+1)\u5904\u6dfb\u52a0'pvalue'\u6587\u672c\uff0c\u5e76\u8bbe\u7f6e\u5b57\u4f53\u52a0\u7c97\u3002<\/span><\/code><code><span class=\"code-snippet_outer\"> #\u7ed8\u5236\u53f3\u8fb9\u7684\u68ee\u6797\u56fe<\/span><\/code><code><span class=\"code-snippet_outer\"> par(mar=c(4,1,2,1),mgp=c(2,0.5,0))<\/span><\/code><code><span class=\"code-snippet_outer\"> xlim = c(0,max(as.numeric(hrLow),as.numeric(hrHigh)))<\/span><\/code><code><span class=\"code-snippet_outer\"> plot(1,xlim=xlim,ylim=ylim,type=\"n\",axes=F,ylab=\"\",xaxs=\"i\",xlab=\"Hazard ratio\")<\/span><\/code><code><span class=\"code-snippet_outer\"> arrows(as.numeric(hrLow),n:1,as.numeric(hrHigh),n:1,angle=90,code=3,length=0.05,col=\"darkblue\",lwd=3)<\/span><\/code><code><span class=\"code-snippet_outer\"> abline(v=1, col=\"black\", lty=2, lwd=2)<\/span><\/code><code><span class=\"code-snippet_outer\"> boxcolor = ifelse(as.numeric(hr) > 1, forestCol, forestCol)<\/span><\/code><code><span class=\"code-snippet_outer\"> points(as.numeric(hr), n:1, pch = 15, col = boxcolor, cex=2)<\/span><\/code><code><span class=\"code-snippet_outer\"> axis(1)<\/span><\/code><code><span class=\"code-snippet_outer\"> dev.off()<\/span><\/code><code><span class=\"code-snippet_outer\">}<\/span><\/code><code><span class=\"code-snippet_outer\">############\u5b9a\u4e49\u68ee\u6797\u56fe\u51fd\u6570############<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">#\u5b9a\u4e49\u72ec\u7acb\u9884\u540e\u5206\u6790\u51fd\u6570<\/span><\/code><code><span class=\"code-snippet_outer\">#\u5b9a\u4e49\u4e86\u4e00\u4e2a\u540d\u4e3aindep\u7684\u51fd\u6570\uff0c\u8be5\u51fd\u6570\u6709\u516d\u4e2a\u53c2\u6570\uff1aexpFile\u3001cliFile\u3001uniOutFile\u3001multiOutFile\u3001uniForest\u548cmultiForest\uff0c<\/span><\/code><code><span class=\"code-snippet_outer\">#\u8fd9\u4e9b\u53c2\u6570\u53ef\u4ee5\u5728\u51fd\u6570\u88ab\u8c03\u7528\u65f6\u4f20\u9012\u5b9e\u9645\u503c\u3002<\/span><\/code><code><span class=\"code-snippet_outer\">indep=function(expFile=null,cliFile=null,uniOutFile=null,multiOutFile=null,uniForest=null,multiForest=null){<\/span><\/code><code><span class=\"code-snippet_outer\"> exp=read.table(expFile, header=T, sep=\"t\", check.names=F, row.names=1) #\u8bfb\u53d6\u8868\u8fbe\u6587\u4ef6<\/span><\/code><code><span class=\"code-snippet_outer\"> cli=read.table(cliFile, header=T, sep=\"t\", check.names=F, row.names=1) #\u8bfb\u53d6\u4e34\u5e8a\u6587\u4ef6<\/span><\/code><code><span class=\"code-snippet_outer\"> #\u7528read.table\u51fd\u6570\u4eceexpFile\u4e2d\u8bfb\u53d6\u6570\u636e\uff0c\u6570\u636e\u4ee5Tab\u5206\u9694\uff0c\u5305\u542b\u8868\u5934\uff08header=T\uff09\uff0c<\/span><\/code><code><span class=\"code-snippet_outer\"> #\u7b2c\u4e00\u5217\u4f5c\u4e3a\u884c\u540d\uff08row.names=1\uff09\uff0c\u5e76\u5c06\u6570\u636e\u4fdd\u5b58\u5230\u540d\u4e3aexp\u7684\u6570\u636e\u6846\u4e2d\u3002<\/span><\/code><code><span class=\"code-snippet_outer\"> #\u7528read.table\u51fd\u6570\u4ececliFile\u4e2d\u8bfb\u53d6\u6570\u636e\uff0c\u6570\u636e\u4ee5Tab\u5206\u9694\uff0c\u5305\u542b\u8868\u5934\uff08header=T\uff09\uff0c<\/span><\/code><code><span class=\"code-snippet_outer\"> #\u7b2c\u4e00\u5217\u4f5c\u4e3a\u884c\u540d\uff08row.names=1\uff09\uff0c\u5e76\u5c06\u6570\u636e\u4fdd\u5b58\u5230\u540d\u4e3acli\u7684\u6570\u636e\u6846\u4e2d\u3002<\/span><\/code><code><span class=\"code-snippet_outer\"> #\u6570\u636e\u5408\u5e76<\/span><\/code><code><span class=\"code-snippet_outer\"> sameSample=intersect(row.names(cli),row.names(exp))<\/span><\/code><code><span class=\"code-snippet_outer\"> #\u83b7\u53d6\u4e24\u4e2a\u6570\u636e\u6846cli\u548cexp\u884c\u540d\uff08\u6837\u672c\u540d\u79f0\uff09\u7684\u4ea4\u96c6\uff0c\u5e76\u4fdd\u5b58\u5230sameSample\u53d8\u91cf\u4e2d\u3002<\/span><\/code><code><span class=\"code-snippet_outer\"> exp=exp[sameSample,]<\/span><\/code><code><span class=\"code-snippet_outer\"> cli=cli[sameSample,]<\/span><\/code><code><span class=\"code-snippet_outer\"> rt=cbind(exp, cli)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"> #\u5355\u56e0\u7d20\u72ec\u7acb\u9884\u540e\u5206\u6790<\/span><\/code><code><span class=\"code-snippet_outer\"> uniTab=data.frame()<\/span><\/code><code><span class=\"code-snippet_outer\"> for(i in colnames(rt[,3:ncol(rt)])){<\/span><\/code><code><span class=\"code-snippet_outer\"> cox <- coxph(Surv(futime, fustat) ~ rt[,i], data = rt)<\/span><\/code><code><span class=\"code-snippet_outer\"> #\u4f7f\u7528coxph\u51fd\u6570\u8fdb\u884cCox\u6bd4\u4f8b\u98ce\u9669\u6a21\u578b\u5206\u6790\uff0c\u5176\u4e2dSurv(futime, fustat)\u8868\u793a\u751f\u5b58\u65f6\u95f4\u548c\u4e8b\u4ef6\u53d1\u751f\u60c5\u51b5\uff0c<\/span><\/code><code><span class=\"code-snippet_outer\"> #rt[,i]\u8868\u793a\u5f53\u524d\u5faa\u73af\u7684\u5217\u4f5c\u4e3a\u9884\u6d4b\u56e0\u5b50\uff0cdata=rt\u8868\u793a\u4f7f\u7528rt\u6570\u636e\u6846\u3002<\/span><\/code><code><span class=\"code-snippet_outer\"> coxSummary = summary(cox)<\/span><\/code><code><span class=\"code-snippet_outer\"> uniTab=rbind(uniTab,<\/span><\/code><code><span class=\"code-snippet_outer\"> cbind(id=i,<\/span><\/code><code><span class=\"code-snippet_outer\"> HR=coxSummary$conf.int[,\"exp(coef)\"],<\/span><\/code><code><span class=\"code-snippet_outer\"> HR.95L=coxSummary$conf.int[,\"lower .95\"],<\/span><\/code><code><span class=\"code-snippet_outer\"> HR.95H=coxSummary$conf.int[,\"upper .95\"],<\/span><\/code><code><span class=\"code-snippet_outer\"> pvalue=coxSummary$coefficients[,\"Pr(>|z|)\"])<\/span><\/code><code><span class=\"code-snippet_outer\"> )<\/span><\/code><code><span class=\"code-snippet_outer\"> }<\/span><\/code><code><span class=\"code-snippet_outer\"> write.table(uniTab,file=uniOutFile,sep=\"t\",row.names=F,quote=F)<\/span><\/code><code><span class=\"code-snippet_outer\"> bioForest(coxFile=uniOutFile, forestFile=uniForest, forestCol=\"green\")<\/span><\/code><\/pre>\n<\/section>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"text-align: center;\"><br \/><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.1791907514450867\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_D6Bjw5jkAZuSz4iaUmjsb0ks7rAqJw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAy6nCYibdkPuFzMl1gf54TicBOt6XTkQJmAKg7HFlZ5lkPPVsXD6Bjw5jkAZuSz4iaUmjsb0ks7rAqJw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"692\" style=\"\" data-recalc-dims=\"1\" \/><\/p>\n<p><br \/><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"php\"><code><span class=\"code-snippet_outer\">#\u591a\u56e0\u7d20\u72ec\u7acb\u9884\u540e\u5206\u6790<\/span><\/code><code><span class=\"code-snippet_outer\"> uniTab=uniTab[as.numeric(uniTab[,\"pvalue\"])<1,]<\/span><\/code><code><span class=\"code-snippet_outer\"> rt1=rt[,c(\"futime\", \"fustat\", as.vector(uniTab[,\"id\"]))]<\/span><\/code><code><span class=\"code-snippet_outer\"> #\u4ecert\u6570\u636e\u6846\u4e2d\u9009\u62e9\"futime\"\u3001\"fustat\"\u548cuniTab\u6570\u636e\u6846\u4e2d\u7684\"pvalue\"\u5217\u5bf9\u5e94\u7684\u9884\u6d4b\u56e0\u5b50\u5217\uff0c<\/span><\/code><code><span class=\"code-snippet_outer\"> #\u5e76\u5c06\u5b83\u4eec\u5408\u5e76\u4e3a\u4e00\u4e2a\u65b0\u7684\u6570\u636e\u6846rt1\u3002<\/span><\/code><code><span class=\"code-snippet_outer\"> multiCox=coxph(Surv(futime, fustat) ~ ., data = rt1)<\/span><\/code><code><span class=\"code-snippet_outer\"> multiCoxSum=summary(multiCox)<\/span><\/code><code><span class=\"code-snippet_outer\"> multiTab=data.frame()<\/span><\/code><code><span class=\"code-snippet_outer\"> multiTab=cbind(<\/span><\/code><code><span class=\"code-snippet_outer\"> HR=multiCoxSum$conf.int[,\"exp(coef)\"],<\/span><\/code><code><span class=\"code-snippet_outer\"> HR.95L=multiCoxSum$conf.int[,\"lower .95\"],<\/span><\/code><code><span class=\"code-snippet_outer\"> HR.95H=multiCoxSum$conf.int[,\"upper .95\"],<\/span><\/code><code><span class=\"code-snippet_outer\"> pvalue=multiCoxSum$coefficients[,\"Pr(>|z|)\"])<\/span><\/code><code><span class=\"code-snippet_outer\"> multiTab=cbind(id=row.names(multiTab),multiTab)<\/span><\/code><code><span class=\"code-snippet_outer\"> write.table(multiTab,file=multiOutFile,sep=\"t\",row.names=F,quote=F)<\/span><\/code><code><span class=\"code-snippet_outer\"> bioForest(coxFile=multiOutFile, forestFile=multiForest, forestCol=\"red\")<\/span><\/code><code><span class=\"code-snippet_outer\">}<\/span><\/code><\/pre>\n<\/section>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.6868475991649269\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_QfYfcqhx7kONFECx80EnRxSnNt9rEA.png?w=640\" 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rel=\"noopener\">1.\u642d\u5efa\u751f\u4fe1\u5206\u6790\u6d41\u6c34\u7ebf\uff0c\u5982\u5de5\u5382\u4e00\u683724\u5c0f\u65f6\u8fd0\u8f6cSnakemake\u2014\u2014\u8fdb\u9636\u547d\u4ee4<\/a><br \/><\/section>\n<section style=\"margin-bottom: 0px;font-size: 16px;letter-spacing: 0.578px;white-space: normal;line-height: 1.75em;\"><a target=\"_blank\" href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247491705&idx=1&sn=9ff9b6da28b3a256a99c6697d589be66&chksm=cf7f70bcf808f9aafd1019a0bba3dd3a55e2867dbb9a09203f13c2683adf867094637c405ed1&scene=21#wechat_redirect\" textvalue=\"2.\u6bd4blast\u8fd8\u4f18\u79c0\u7684\u5e8f\u5217\u6bd4\u5bf9\u5de5\u5177\uff1fHMMER\u6765\u4e86\" linktype=\"text\" imgurl=\"\" imgdata=\"null\" data-itemshowtype=\"0\" tab=\"innerlink\" data-linktype=\"2\" rel=\"noopener\">2.\u6bd4blast\u8fd8\u4f18\u79c0\u7684\u5e8f\u5217\u6bd4\u5bf9\u5de5\u5177\uff1fHMMER\u6765\u4e86<\/a><\/section>\n<section style=\"margin-bottom: 0px;font-size: 16px;letter-spacing: 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16px;\">\n<section>\n<section style=\"margin-top: 0.5em;\">\n<section style=\"padding: 0.5em;border-width: 1px;border-style: solid;box-shadow: rgb(226, 226, 226) 0px 16px 1px -13px;border-color: rgb(0, 150, 136);\">\n<section style=\"text-align: left;\">\n<section style=\"color: rgb(255, 129, 36);text-align: justify;\">\n<section style=\"margin-bottom: 8px;\">\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"letter-spacing: 0.5px;\">\u70b9\u51fb<strong><span style=\"color: rgb(0, 150, 136);\">\u201c\u9605\u8bfb\u539f\u6587\u201d<\/span><\/strong>\u7acb\u523b\u62e5\u6709<\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"margin-bottom: 8px;font-size: 32px;color: rgb(0, 150, 136);\">\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"letter-spacing: 0.5px;\">\u2193\u2193\u2193 <\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p style=\"display: none;\"><mp-style-type data-value=\"3\"><\/mp-style-type><\/p>\n<div class=\"msg_source_url\"><a href=\"https:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247493050&idx=2&sn=ee0643e61ad49d9da96fc5ead974bd8b&chksm=cf7f757ff808fc69c274f50b85b15bb7afae13df06337fb3cdc26bfb38fbc17b8bc48b37e65a&token=1057101627&lang=zh_CN#rd\" target=\"_blank\" rel=\"noopener\">\u9605\u8bfb\u539f\u6587<\/a><\/div>\n<p><\/content><\/p>\n<div class=\"msg_source_url\"><a href=\"https:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247493050&idx=2&sn=ee0643e61ad49d9da96fc5ead974bd8b&chksm=cf7f757ff808fc69c274f50b85b15bb7afae13df06337fb3cdc26bfb38fbc17b8bc48b37e65a&token=1057101627&lang=zh_CN#rd\" target=\"_blank\" rel=\"noopener\">\u9605\u8bfb\u539f\u6587<\/a><\/div>\n<\/div>\n<p><\/body><br 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[…]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"","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\/59757"}],"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=59757"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/59757\/revisions"}],"predecessor-version":[{"id":59764,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/59757\/revisions\/59764"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=59757"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=59757"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=59757"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}