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\u4ee3\u7801\u6839\u636e\u6bcf\u4e2a\u57fa\u56e0\u7684\u8868\u8fbe\u6c34\u5e73\uff0c\u5206\u522b\u6784\u5efaCox\u6bd4\u4f8b\u98ce\u9669\u6a21\u578b\u3002\u8fd9\u4e9b\u6a21\u578b\u7528\u4e8e\u8bc4\u4f30\u6bcf\u4e2a\u57fa\u56e0\u662f\u5426\u4e0e\u751f\u5b58\u7387\u76f8\u5173\u3002\u5982\u679c\u67d0\u4e2a\u57fa\u56e0\u7684\u8868\u8fbe\u4e0e\u751f\u5b58\u7387\u663e\u8457\u76f8\u5173\uff08\u6ee1\u8db3p\u503c\u8fc7\u6ee4\u6761\u4ef6\uff09\uff0c\u5219\u8ba4\u4e3a\u8be5\u57fa\u56e0\u5728\u751f\u5b58\u9884\u540e\u4e2d\u53ef\u80fd\u5177\u6709\u91cd\u8981\u610f\u4e49\u3002<\/p>\n <\/p>\n\u751f\u5b58\u5206\u6790\uff1a<\/strong> \u4ee3\u7801\u4f7f\u7528survival\u5305\u5bf9\u7ed9\u5b9a\u7684\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u548c\u4e34\u5e8a\u6570\u636e\u8fdb\u884c\u751f\u5b58\u5206\u6790\u3002\u751f\u5b58\u5206\u6790\u662f\u4e00\u79cd\u7edf\u8ba1\u65b9\u6cd5\uff0c\u7528\u4e8e\u8bc4\u4f30\u4e0d\u540c\u53d8\u91cf\uff08\u4f8b\u5982\u57fa\u56e0\u8868\u8fbe\uff09\u4e0e\u751f\u5b58\u671f\u4e4b\u95f4\u7684\u5173\u8054\u3002\u901a\u8fc7\u6784\u5efaCox\u6bd4\u4f8b\u98ce\u9669\u6a21\u578b\uff0c\u4ee3\u7801\u63a2\u7d22\u4e86\u5355\u4e2a\u57fa\u56e0\u8868\u8fbe\u548c\u751f\u5b58\u4e4b\u95f4\u7684\u53ef\u80fd\u5173\u7cfb\u3002<\/p>\n<\/section>\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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code>#install.packages('survival')<\/span><\/span><\/code><code>#\u7528library()\u51fd\u6570\u52a0\u8f7dsurvival\u5305\u3002<\/span><\/span><\/code><code>library(survival)<\/span><\/code><code>expFile=\"surSigExp.txt\"<\/span><\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.5209876543209877\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_6ZPGGibLsBCaHYNb58YAkuseYo3HOg.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEX2ibTZqqt1FbZ0Xx0iclEKc387hwwztAM6t4Qt07vFyShNjbQ6ZPGGibLsBCaHYNb58YAkuseYo3HOg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"810\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code>#\u8868\u8fbe\u6570\u636e\u6587\u4ef6<\/span><\/span><\/code><code>clinicalFile=\"clinicalNum.txt\"<\/span><\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.8971774193548387\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-08-26_\u300c\u8f6c\u300d\u7eaf\u4ee3\u7801\uff0c\u5e08\u59b9\u5e26\u4f60\u8f7b\u677e\u73a9\u8f6c\u751f\u5b58\u5206\u6790\u4e4b\u72ec\u7acb\u9884\u540e\u5206\u6790\/2_Mocb4uz3gk04gs1UmaicMQZPWDokPQ.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEX2ibTZqqt1FbZ0Xx0iclEKc3ibaicbfvghWRSOys8zKLyXDx8RHMocb4uz3gk04gs1UmaicMQZPWDokPQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"496\" style=\"vertical-align: middle;width: 100%;\" \/><\/section>\n<\/section>\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<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=\"r\"><code>#\u4e34\u5e8a\u6570\u636e\u6587\u4ef6<\/span><\/span><\/code><code>#\u7531expFile\u548cclinicalFile\u53d8\u91cf\u6307\u5b9a\u7684\u6587\u4ef6\u4e2d\u8bfb\u53d6\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u548c\u4e34\u5e8a\u6570\u636e\u3002<\/span><\/span><\/code><code>exp<\/span>=read.table(expFile,sep=\"t\"<\/span>,header=T<\/span>,check.names=F<\/span>,row.names=1<\/span>) #\u8bfb\u53d6\u8868\u8fbe\u6570\u636e\u6587\u4ef6<\/span><\/span><\/code><code>cli=read.table(clinicalFile,sep=\"t\"<\/span>,header=T<\/span>,check.names=F<\/span>,row.names=1<\/span>) #\u8bfb\u53d6\u4e34\u5e8a\u6570\u636e\u6587\u4ef6<\/span><\/span><\/code><code>samSample=intersect(row.names(exp<\/span>),row.names(cli))<\/span><\/code><code>exp<\/span>=exp<\/span>[samSample,]<\/span><\/code><code>cli=cli[samSample,]<\/span><\/code><code>pFilter=0.05<\/span> #p\u503c\u8fc7\u6ee4\u6761\u4ef6<\/span><\/span><\/code><code>#\u53d8\u91cfpFilter\u8bbe\u7f6e\u4e3a\u663e\u8457\u6027\u9608\u503c\uff0c\u7528\u4e8ep\u503c<\/span><\/span><\/code><code> <\/span><\/code><code>############\u7ed8\u5236\u68ee\u6797\u56fe\u51fd\u6570############<\/span><\/span><\/code><code>bioForest=function<\/span>(coxFile=null,forestFile=null,forestCol=null){<\/span><\/code><code># \u5b9a\u4e49\u81ea\u5b9a\u4e49\u51fd\u6570bioForest\uff0c\u7528\u4e8e\u4eceCox\u6bd4\u4f8b\u98ce\u9669\u6a21\u578b\u7ed3\u679c\u521b\u5efa\u68ee\u6797\u56fe\u3002<\/span><\/span><\/code><code># \u6b64\u51fd\u6570\u63a5\u53d7\u53c2\u6570\uff0c\u5982coxFile\uff08Cox\u6a21\u578b\u7ed3\u679c\u6587\u4ef6\uff09\u3001forestFile\uff08\u8f93\u51faPDF\u6587\u4ef6\uff09\u548cforestCol\uff08\u68ee\u6797\u56fe\u6846\u7684\u989c\u8272\uff09\u3002<\/span><\/span><\/code><code>#\u8bfb\u53d6\u8f93\u5165\u6587\u4ef6<\/span><\/span><\/code><code>rt <- read.table(coxFile,header=T<\/span>,sep=\"t\"<\/span>,row.names=1<\/span>,check.names=F<\/span>)<\/span><\/code><code>gene <- rownames(rt)<\/span><\/code><code>#\u5faa\u73af\u904d\u5386\u8868\u8fbe\u6570\u636e\u4e2d\u7684\u6bcf\u4e2a\u57fa\u56e0\u3002<\/span><\/span><\/code><code>hr <- sprintf(\"%.3f\"<\/span>,rt$\"HR\"<\/span>)<\/span><\/code><code>hrLow <- sprintf(\"%.3f\"<\/span>,rt$\"HR.95L\"<\/span>)<\/span><\/code><code>hrHigh <- sprintf(\"%.3f\"<\/span>,rt$\"HR.95H\"<\/span>)<\/span><\/code><code>Hazard.ratio <- paste0(hr,\"(\"<\/span>,hrLow,\"-\"<\/span>,hrHigh,\")\"<\/span>)<\/span><\/code><code>pVal <- ifelse(rt$pvalue<0.001<\/span>, \"<0.001\"<\/span>, sprintf(\"%.3f\"<\/span>, rt$pvalue))<\/span><\/code><code> <\/span><\/code><code>#\u8f93\u51fa\u56fe\u5f62<\/span><\/span><\/code><code>pdf(file=forestFile, width = 7<\/span>,height = 4.5<\/span>)<\/span><\/code><code>n <- nrow(rt)<\/span><\/code><code>nRow <- n+1<\/span><\/span><\/code><code>ylim <- c<\/span>(1<\/span>,nRow)<\/span><\/code><code>layout(matrix(c<\/span>(1<\/span>,2<\/span>),nc=2<\/span>),width=c<\/span>(3<\/span>,2.5<\/span>))<\/span><\/code><code> <\/span><\/code><code>#\u7ed8\u5236\u68ee\u6797\u56fe\u5de6\u8fb9\u7684\u4e34\u5e8a\u4fe1\u606f<\/span><\/span><\/code><code>xlim = c<\/span>(0<\/span>,3<\/span>)<\/span><\/code><code>par(mar=c<\/span>(4<\/span>,2.5<\/span>,2<\/span>,1<\/span>))<\/span><\/code><code>plot(1<\/span>,xlim=xlim,ylim=ylim,type=\"n\"<\/span>,axes=F<\/span>,xlab=\"\"<\/span>,ylab=\"\"<\/span>)<\/span><\/code><code>text.cex=0.8<\/span><\/span><\/code><code>text(0<\/span>,n:1<\/span>,gene,adj=0<\/span>,cex=text.cex)<\/span><\/code><code>text(1.5<\/span>-0.5<\/span>*0.2<\/span>,n:1<\/span>,pVal,adj=1<\/span>,cex=text.cex);text(1.5<\/span>-0.5<\/span>*0.2<\/span>,n+1<\/span>,'pvalue'<\/span>,cex=text.cex,font=2<\/span>,adj=1<\/span>)<\/span><\/code><code>text(3<\/span>,n:1<\/span>,Hazard.ratio,adj=1<\/span>,cex=text.cex);text(3<\/span>,n+1<\/span>,'Hazard ratio'<\/span>,cex=text.cex,font=2<\/span>,adj=1<\/span>,)<\/span><\/code><code> <\/span><\/code><code>#\u7ed8\u5236\u68ee\u6797\u56fe<\/span><\/span><\/code><code>par(mar=c<\/span>(4<\/span>,1<\/span>,2<\/span>,1<\/span>),mgp=c<\/span>(2<\/span>,0.5<\/span>,0<\/span>))<\/span><\/code><code>xlim = c<\/span>(0<\/span>,max<\/span>(as.numeric<\/span>(hrLow),as.numeric<\/span>(hrHigh)))<\/span><\/code><code>plot(1<\/span>,xlim=xlim,ylim=ylim,type=\"n\"<\/span>,axes=F<\/span>,ylab=\"\"<\/span>,xaxs=\"i\"<\/span>,xlab=\"Hazard ratio\"<\/span>)<\/span><\/code><code>arrows(as.numeric<\/span>(hrLow),n:1<\/span>,as.numeric<\/span>(hrHigh),n:1<\/span>,angle=90<\/span>,code=3<\/span>,length<\/span>=0.05<\/span>,col=\"darkblue\"<\/span>,lwd=2.5<\/span>)<\/span><\/code><code>abline(v=1<\/span>,col=\"black\"<\/span>,lty=2<\/span>,lwd=2<\/span>)<\/span><\/code><code>boxcolor = ifelse(as.numeric<\/span>(hr) > 1<\/span>, forestCol, forestCol)<\/span><\/code><code>points(as.numeric<\/span>(hr), n:1<\/span>, pch = 15<\/span>, col = boxcolor, cex=1.3<\/span>)<\/span><\/code><code>axis(1<\/span>)<\/span><\/code><code>dev.off()<\/span><\/code><code>}<\/span><\/code><code>############\u7ed8\u5236\u68ee\u6797\u56fe\u51fd\u6570############<\/span><\/span><\/code><code>#\u72ec\u7acb\u9884\u540e\u5206\u6790\uff0c\u8f93\u51fa\u8868\u683c<\/span><\/span><\/code><code>allOutTab=data.frame()<\/span><\/code><code>#\u521d\u59cb\u5316\u4e00\u4e2a\u7a7a\u7684\u6570\u636e\u6846 allOutTab\uff0c\u7528\u4e8e\u5b58\u50a8\u72ec\u7acb\u9884\u540e\u5206\u6790\u7684\u7ed3\u679c<\/span><\/span><\/code><code>sigGenes=c<\/span>(\"futime\"<\/span>,\"fustat\"<\/span>)<\/span><\/code><code>#\u4e00\u4e2a\u5b57\u7b26\u5411\u91cf sigGenes\uff0c\u5176\u4e2d\u5305\u542b\u521d\u59cb\u7684\u4e24\u4e2a\u5217\u540d \"futime\" \u548c \"fustat\"\uff0c\u8fd9\u4e9b\u5217\u7528\u4e8e\u6784\u5efa Cox \u6bd4\u4f8b\u98ce\u9669\u6a21\u578b\u3002<\/span><\/span><\/code><code>for<\/span>(i in<\/span> colnames(exp<\/span>[,3<\/span>:ncol(exp<\/span>)])){<\/span><\/code><code>#\u5faa\u73af\u904d\u5386\u8868\u8fbe\u6570\u636e\u7684\u5217\uff0c\u5176\u4e2d\u5305\u62ec\u5177\u4f53\u7684\u57fa\u56e0\u8868\u8fbe\u4fe1\u606f\u3002<\/span><\/span><\/code><code>#\u9488\u5bf9\u6bcf\u4e2a\u57fa\u56e0\uff0c\u6784\u5efa Cox \u6bd4\u4f8b\u98ce\u9669\u6a21\u578b\uff0c\u5e76\u5bf9\u6a21\u578b\u7684\u7ed3\u679c\u8fdb\u884c\u603b\u7ed3\uff08summary\uff09\u3002<\/span><\/span><\/code><code>rt=cbind(exp<\/span>[,1<\/span>:2<\/span>],cli,gene=exp<\/span>[,i])<\/span><\/code><code>colnames(rt)[ncol(rt)]=i<\/span><\/code><code>cox <- coxph(Surv(futime, fustat) ~ rt[,ncol(rt)], data = rt)<\/span><\/code><code>coxSummary = summary(cox)<\/span><\/code><code>outTab=data.frame()<\/span><\/code><code># p \u503c\u5c0f\u4e8e\u9884\u8bbe\u7684\u8fc7\u6ee4\u6761\u4ef6\uff08pFilter\uff09\uff0c\u5219\u7ee7\u7eed\u5728\u5185\u90e8\u5faa\u73af\u4e2d\uff0c\u5206\u522b\u6784\u5efa\u53ea\u5305\u542b\u4e00\u4e2a\u57fa\u56e0\u8868\u8fbe\u53d8\u91cf\u7684 Cox \u6bd4\u4f8b\u98ce\u9669\u6a21\u578b\u3002<\/span><\/span><\/code><code>if<\/span>(coxSummary$coefficients[,\"Pr(>|z|)\"<\/span>]<\/span><\/code><code>for<\/span>(j in<\/span> colnames(rt[,3<\/span>:ncol(rt)])){<\/span><\/code><code>coxJ <- coxph(Surv(futime, fustat) ~ rt[,j], data = rt)<\/span><\/code><code>coxSummaryJ = summary(coxJ)<\/span><\/code><code>coxP=coxSummaryJ$coefficients[,\"Pr(>|z|)\"<\/span>]<\/span><\/code><code>if<\/span>(coxSummaryJ$conf.int[,\"upper .95\"<\/span>] != Inf<\/span>){<\/span><\/code><code>outTab=rbind(outTab,<\/span><\/code><code>cbind(id=j,<\/span><\/code><code>HR=coxSummaryJ$conf.int[,\"exp(coef)\"<\/span>],<\/span><\/code><code>HR.95L=coxSummaryJ$conf.int[,\"lower .95\"<\/span>],<\/span><\/code><code>HR.95H=coxSummaryJ$conf.int[,\"upper .95\"<\/span>],<\/span><\/code><code>pvalue=coxSummaryJ$coefficients[,\"Pr(>|z|)\"<\/span>])<\/span><\/code><code>)<\/span><\/code><code>}<\/span><\/code><code>}<\/span><\/code><code>write.table(outTab,file=\"uniCox.txt\"<\/span>,sep=\"t\"<\/span>,row.names=F<\/span>,quote<\/span>=F<\/span>)<\/span><\/code><code>bioForest(coxFile=\"uniCox.txt\"<\/span>,forestFile=paste0(\"uni.\"<\/span>,i,\".pdf\"<\/span>),forestCol=\"green\"<\/span>)<\/span><\/code><code>unlink(\"uniCox.txt\"<\/span>)<\/span><\/code><code> <\/span><\/code><code>sigGenes=c<\/span>(sigGenes,i)<\/span><\/code><code>allOutTab=rbind(allOutTab,<\/span><\/code><code>cbind(id=i,<\/span><\/code><code>HR=coxSummary$conf.int[,\"exp(coef)\"<\/span>],<\/span><\/code><code>HR.95L=coxSummary$conf.int[,\"lower .95\"<\/span>],<\/span><\/code><code>HR.95H=coxSummary$conf.int[,\"upper .95\"<\/span>],<\/span><\/code><code>pvalue=coxSummary$coefficients[,\"Pr(>|z|)\"<\/span>])<\/span><\/code><code>)<\/span><\/code><code>}<\/span><\/code><code>}<\/span><\/code><code>#\u8f93\u51fa\u5355\u56e0\u7d20\u72ec\u7acb\u9884\u540e\u5206\u6790\u7ed3\u679c<\/span><\/span><\/code><code>write.table(allOutTab,file=\"uniIndep.xls\"<\/span>,sep=\"t\"<\/span>,row.names=F<\/span>,quote<\/span>=F<\/span>)<\/span><\/code><code>#\u8f93\u51fa\u5355\u56e0\u7d20\u72ec\u7acb\u9884\u540e\u57fa\u56e0\u8868\u8fbe\u91cf<\/span><\/span><\/code><code>indepSigExp=exp<\/span>[,sigGenes]<\/span><\/code><code>indepSigExp=cbind(id=row.names(indepSigExp),indepSigExp)<\/span><\/code><code>write.table(indepSigExp,file=\"uniIndepSigExp.txt\"<\/span>,sep=\"t\"<\/span>,row.names=F<\/span>,quote<\/span>=F<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.5142150803461063\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-08-26_\u300c\u8f6c\u300d\u7eaf\u4ee3\u7801\uff0c\u5e08\u59b9\u5e26\u4f60\u8f7b\u677e\u73a9\u8f6c\u751f\u5b58\u5206\u6790\u4e4b\u72ec\u7acb\u9884\u540e\u5206\u6790\/3_BkhxaR1ibD2xsWdEiaCYjJAiaB1x2w.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEX2ibTZqqt1FbZ0Xx0iclEKc3E1ic1Kn8F4Ow8DroVlGQVGE1qcpuBkhxaR1ibD2xsWdEiaCYjJAiaB1x2w\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"809\" style=\"vertical-align: middle;width: 100%;\" \/><\/section>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"2.239130434782609\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_mw5ic0n1lGIYQK8zfsHz4oicwtcsog.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEX2ibTZqqt1FbZ0Xx0iclEKc3lKWsWVOjG6W8fNHcXNly14y1OXmw5ic0n1lGIYQK8zfsHz4oicwtcsog\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"276\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.6136363636363636\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_jsfzwfOfJfRarEObaiaqdscoS92NUw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEX2ibTZqqt1FbZ0Xx0iclEKc3VcVY4EepWPLBgbXfiaXuGy7ibagjsfzwfOfJfRarEObaiaqdscoS92NUw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"660\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.6111951588502269\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-08-26_\u300c\u8f6c\u300d\u7eaf\u4ee3\u7801\uff0c\u5e08\u59b9\u5e26\u4f60\u8f7b\u677e\u73a9\u8f6c\u751f\u5b58\u5206\u6790\u4e4b\u72ec\u7acb\u9884\u540e\u5206\u6790\/6_dV6fhHicZkib7scAicnGdr5miaAa7A.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEX2ibTZqqt1FbZ0Xx0iclEKc3OaLjKMsNDUzSzFbXYb8K5nKJbySmdV6fhHicZkib7scAicnGdr5miaAa7A\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"661\" style=\"vertical-align: middle;width: 100%;\" \/><\/section>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.6196969696969697\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/7_dBLnol4uor9bK9wD4GkxaTbm5iazgg.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEX2ibTZqqt1FbZ0Xx0iclEKc3qRqMak4jsUqGPrriaiaT2OV7r8fdBLnol4uor9bK9wD4GkxaTbm5iazgg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"660\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section powered-by=\"xiumi.us\">\n\u5c06\u72ec\u7acb\u9884\u540e\u5206\u6790\u7684\u7ed3\u679c\u5199\u5165\u540d\u4e3a “uniIndep.xls” \u7684\u6587\u4ef6\u4e2d\uff0c\u5176\u4e2d\u5305\u62ec\u6bcf\u4e2a\u57fa\u56e0\u7684Hazard Ratio\u3001\u7f6e\u4fe1\u533a\u95f4\u548cp\u503c\u7b49\u4fe1\u606f\u3002\u6b64\u5916\uff0c\u4ee3\u7801\u8fd8\u5c06\u6ee1\u8db3\u663e\u8457\u6027\u6761\u4ef6\u7684\u57fa\u56e0\u7684\u8868\u8fbe\u6570\u636e\u5199\u5165\u540d\u4e3a “uniIndepSigExp.txt” \u7684\u6587\u4ef6\u4e2d\u3002<\/p>\n 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{"id":58726,"date":"2024-06-16T23:22:49","date_gmt":"2024-06-16T15:22:49","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=58726"},"modified":"2024-06-16T23:22:49","modified_gmt":"2024-06-16T15:22:49","slug":"%e7%ba%af%e4%bb%a3%e7%a0%81%ef%bc%8c%e5%b8%88%e5%a6%b9%e5%b8%a6%e4%bd%a0%e8%bd%bb%e6%9d%be%e7%8e%a9%e8%bd%ac%e7%94%9f%e5%ad%98%e5%88%86%e6%9e%90%e4%b9%8b%e7%8b%ac%e7%ab%8b%e9%a2%84%e5%90%8e%e5%88%86-2","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=58726","title":{"rendered":"\u7eaf\u4ee3\u7801\uff0c\u5e08\u59b9\u5e26\u4f60\u8f7b\u677e\u73a9\u8f6c\u751f\u5b58\u5206\u6790\u4e4b\u72ec\u7acb\u9884\u540e\u5206\u6790"},"content":{"rendered":"

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-14px;\" powered-by=\"xiumi.us\">\n{ \u70b9\u51fb\u84dd\u5b57\uff0c\u5173\u6ce8\u6211\u4eec }<\/p>\n<\/section>\n<\/section>\n<\/section>\n<section powered-by=\"xiumi.us\">\n\u4e4b\u524d\u5c0f\u5e08\u59b9\u5e26\u5927\u5bb6\u505a\u8fc7\u4e86\u68ee\u6797\u56fe\u7684\u7ed8\u5236\uff0c\u90a3\u4e48\u4eca\u5929\u6211\u4eec\u518d\u6765\u5b9e\u64cd\u751f\u5b58\u5206\u6790\u7684\u72ec\u7acb\u9884\u540e\u5206\u6790\uff0c\u5bfb\u627e\u4e0e\u751f\u5b58\u671f\u76f8\u5173\u7684\u57fa\u56e0\uff0c\u5e76\u751f\u6210\u76f8\u5e94\u7684\u68ee\u6797\u56fe\uff0c\u4ece\u800c\u63ed\u793a\u8fd9\u4e9b\u57fa\u56e0\u5bf9\u751f\u5b58\u7387\u7684\u5f71\u54cd\u3002\u5148\u590d\u4e60\u4e86\u89e3\u4e00\u4e0b\u76f8\u5173\u7684\u6982\u5ff5\u3002<\/span><\/p>\n <\/span><\/p>\n\u72ec\u7acb\u9884\u540e\u5206\u6790\uff1a<\/strong> \u4ee3\u7801\u6839\u636e\u6bcf\u4e2a\u57fa\u56e0\u7684\u8868\u8fbe\u6c34\u5e73\uff0c\u5206\u522b\u6784\u5efaCox\u6bd4\u4f8b\u98ce\u9669\u6a21\u578b\u3002\u8fd9\u4e9b\u6a21\u578b\u7528\u4e8e\u8bc4\u4f30\u6bcf\u4e2a\u57fa\u56e0\u662f\u5426\u4e0e\u751f\u5b58\u7387\u76f8\u5173\u3002\u5982\u679c\u67d0\u4e2a\u57fa\u56e0\u7684\u8868\u8fbe\u4e0e\u751f\u5b58\u7387\u663e\u8457\u76f8\u5173\uff08\u6ee1\u8db3p\u503c\u8fc7\u6ee4\u6761\u4ef6\uff09\uff0c\u5219\u8ba4\u4e3a\u8be5\u57fa\u56e0\u5728\u751f\u5b58\u9884\u540e\u4e2d\u53ef\u80fd\u5177\u6709\u91cd\u8981\u610f\u4e49\u3002<\/p>\n <\/p>\n\u751f\u5b58\u5206\u6790\uff1a<\/strong> \u4ee3\u7801\u4f7f\u7528survival\u5305\u5bf9\u7ed9\u5b9a\u7684\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u548c\u4e34\u5e8a\u6570\u636e\u8fdb\u884c\u751f\u5b58\u5206\u6790\u3002\u751f\u5b58\u5206\u6790\u662f\u4e00\u79cd\u7edf\u8ba1\u65b9\u6cd5\uff0c\u7528\u4e8e\u8bc4\u4f30\u4e0d\u540c\u53d8\u91cf\uff08\u4f8b\u5982\u57fa\u56e0\u8868\u8fbe\uff09\u4e0e\u751f\u5b58\u671f\u4e4b\u95f4\u7684\u5173\u8054\u3002\u901a\u8fc7\u6784\u5efaCox\u6bd4\u4f8b\u98ce\u9669\u6a21\u578b\uff0c\u4ee3\u7801\u63a2\u7d22\u4e86\u5355\u4e2a\u57fa\u56e0\u8868\u8fbe\u548c\u751f\u5b58\u4e4b\u95f4\u7684\u53ef\u80fd\u5173\u7cfb\u3002<\/p>\n<\/section>\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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code>#install.packages('survival')<\/span><\/span><\/code><code>#\u7528library()\u51fd\u6570\u52a0\u8f7dsurvival\u5305\u3002<\/span><\/span><\/code><code>library(survival)<\/span><\/code><code>expFile=\"surSigExp.txt\"<\/span><\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.5209876543209877\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_6ZPGGibLsBCaHYNb58YAkuseYo3HOg.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEX2ibTZqqt1FbZ0Xx0iclEKc387hwwztAM6t4Qt07vFyShNjbQ6ZPGGibLsBCaHYNb58YAkuseYo3HOg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"810\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code>#\u8868\u8fbe\u6570\u636e\u6587\u4ef6<\/span><\/span><\/code><code>clinicalFile=\"clinicalNum.txt\"<\/span><\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.8971774193548387\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-08-26_\u300c\u8f6c\u300d\u7eaf\u4ee3\u7801\uff0c\u5e08\u59b9\u5e26\u4f60\u8f7b\u677e\u73a9\u8f6c\u751f\u5b58\u5206\u6790\u4e4b\u72ec\u7acb\u9884\u540e\u5206\u6790\/2_Mocb4uz3gk04gs1UmaicMQZPWDokPQ.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEX2ibTZqqt1FbZ0Xx0iclEKc3ibaicbfvghWRSOys8zKLyXDx8RHMocb4uz3gk04gs1UmaicMQZPWDokPQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"496\" style=\"vertical-align: middle;width: 100%;\" \/><\/section>\n<\/section>\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<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=\"r\"><code>#\u4e34\u5e8a\u6570\u636e\u6587\u4ef6<\/span><\/span><\/code><code>#\u7531expFile\u548cclinicalFile\u53d8\u91cf\u6307\u5b9a\u7684\u6587\u4ef6\u4e2d\u8bfb\u53d6\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u548c\u4e34\u5e8a\u6570\u636e\u3002<\/span><\/span><\/code><code>exp<\/span>=read.table(expFile,sep=\"t\"<\/span>,header=T<\/span>,check.names=F<\/span>,row.names=1<\/span>) #\u8bfb\u53d6\u8868\u8fbe\u6570\u636e\u6587\u4ef6<\/span><\/span><\/code><code>cli=read.table(clinicalFile,sep=\"t\"<\/span>,header=T<\/span>,check.names=F<\/span>,row.names=1<\/span>) #\u8bfb\u53d6\u4e34\u5e8a\u6570\u636e\u6587\u4ef6<\/span><\/span><\/code><code>samSample=intersect(row.names(exp<\/span>),row.names(cli))<\/span><\/code><code>exp<\/span>=exp<\/span>[samSample,]<\/span><\/code><code>cli=cli[samSample,]<\/span><\/code><code>pFilter=0.05<\/span> #p\u503c\u8fc7\u6ee4\u6761\u4ef6<\/span><\/span><\/code><code>#\u53d8\u91cfpFilter\u8bbe\u7f6e\u4e3a\u663e\u8457\u6027\u9608\u503c\uff0c\u7528\u4e8ep\u503c<\/span><\/span><\/code><code> <\/span><\/code><code>############\u7ed8\u5236\u68ee\u6797\u56fe\u51fd\u6570############<\/span><\/span><\/code><code>bioForest=function<\/span>(coxFile=null,forestFile=null,forestCol=null){<\/span><\/code><code># \u5b9a\u4e49\u81ea\u5b9a\u4e49\u51fd\u6570bioForest\uff0c\u7528\u4e8e\u4eceCox\u6bd4\u4f8b\u98ce\u9669\u6a21\u578b\u7ed3\u679c\u521b\u5efa\u68ee\u6797\u56fe\u3002<\/span><\/span><\/code><code># \u6b64\u51fd\u6570\u63a5\u53d7\u53c2\u6570\uff0c\u5982coxFile\uff08Cox\u6a21\u578b\u7ed3\u679c\u6587\u4ef6\uff09\u3001forestFile\uff08\u8f93\u51faPDF\u6587\u4ef6\uff09\u548cforestCol\uff08\u68ee\u6797\u56fe\u6846\u7684\u989c\u8272\uff09\u3002<\/span><\/span><\/code><code>#\u8bfb\u53d6\u8f93\u5165\u6587\u4ef6<\/span><\/span><\/code><code>rt <- read.table(coxFile,header=T<\/span>,sep=\"t\"<\/span>,row.names=1<\/span>,check.names=F<\/span>)<\/span><\/code><code>gene <- rownames(rt)<\/span><\/code><code>#\u5faa\u73af\u904d\u5386\u8868\u8fbe\u6570\u636e\u4e2d\u7684\u6bcf\u4e2a\u57fa\u56e0\u3002<\/span><\/span><\/code><code>hr <- sprintf(\"%.3f\"<\/span>,rt$\"HR\"<\/span>)<\/span><\/code><code>hrLow <- sprintf(\"%.3f\"<\/span>,rt$\"HR.95L\"<\/span>)<\/span><\/code><code>hrHigh <- sprintf(\"%.3f\"<\/span>,rt$\"HR.95H\"<\/span>)<\/span><\/code><code>Hazard.ratio <- paste0(hr,\"(\"<\/span>,hrLow,\"-\"<\/span>,hrHigh,\")\"<\/span>)<\/span><\/code><code>pVal <- ifelse(rt$pvalue<0.001<\/span>, \"<0.001\"<\/span>, sprintf(\"%.3f\"<\/span>, rt$pvalue))<\/span><\/code><code> <\/span><\/code><code>#\u8f93\u51fa\u56fe\u5f62<\/span><\/span><\/code><code>pdf(file=forestFile, width = 7<\/span>,height = 4.5<\/span>)<\/span><\/code><code>n <- nrow(rt)<\/span><\/code><code>nRow <- n+1<\/span><\/span><\/code><code>ylim <- c<\/span>(1<\/span>,nRow)<\/span><\/code><code>layout(matrix(c<\/span>(1<\/span>,2<\/span>),nc=2<\/span>),width=c<\/span>(3<\/span>,2.5<\/span>))<\/span><\/code><code> <\/span><\/code><code>#\u7ed8\u5236\u68ee\u6797\u56fe\u5de6\u8fb9\u7684\u4e34\u5e8a\u4fe1\u606f<\/span><\/span><\/code><code>xlim = c<\/span>(0<\/span>,3<\/span>)<\/span><\/code><code>par(mar=c<\/span>(4<\/span>,2.5<\/span>,2<\/span>,1<\/span>))<\/span><\/code><code>plot(1<\/span>,xlim=xlim,ylim=ylim,type=\"n\"<\/span>,axes=F<\/span>,xlab=\"\"<\/span>,ylab=\"\"<\/span>)<\/span><\/code><code>text.cex=0.8<\/span><\/span><\/code><code>text(0<\/span>,n:1<\/span>,gene,adj=0<\/span>,cex=text.cex)<\/span><\/code><code>text(1.5<\/span>-0.5<\/span>*0.2<\/span>,n:1<\/span>,pVal,adj=1<\/span>,cex=text.cex);text(1.5<\/span>-0.5<\/span>*0.2<\/span>,n+1<\/span>,'pvalue'<\/span>,cex=text.cex,font=2<\/span>,adj=1<\/span>)<\/span><\/code><code>text(3<\/span>,n:1<\/span>,Hazard.ratio,adj=1<\/span>,cex=text.cex);text(3<\/span>,n+1<\/span>,'Hazard ratio'<\/span>,cex=text.cex,font=2<\/span>,adj=1<\/span>,)<\/span><\/code><code> <\/span><\/code><code>#\u7ed8\u5236\u68ee\u6797\u56fe<\/span><\/span><\/code><code>par(mar=c<\/span>(4<\/span>,1<\/span>,2<\/span>,1<\/span>),mgp=c<\/span>(2<\/span>,0.5<\/span>,0<\/span>))<\/span><\/code><code>xlim = c<\/span>(0<\/span>,max<\/span>(as.numeric<\/span>(hrLow),as.numeric<\/span>(hrHigh)))<\/span><\/code><code>plot(1<\/span>,xlim=xlim,ylim=ylim,type=\"n\"<\/span>,axes=F<\/span>,ylab=\"\"<\/span>,xaxs=\"i\"<\/span>,xlab=\"Hazard ratio\"<\/span>)<\/span><\/code><code>arrows(as.numeric<\/span>(hrLow),n:1<\/span>,as.numeric<\/span>(hrHigh),n:1<\/span>,angle=90<\/span>,code=3<\/span>,length<\/span>=0.05<\/span>,col=\"darkblue\"<\/span>,lwd=2.5<\/span>)<\/span><\/code><code>abline(v=1<\/span>,col=\"black\"<\/span>,lty=2<\/span>,lwd=2<\/span>)<\/span><\/code><code>boxcolor = ifelse(as.numeric<\/span>(hr) > 1<\/span>, forestCol, forestCol)<\/span><\/code><code>points(as.numeric<\/span>(hr), n:1<\/span>, pch = 15<\/span>, col = boxcolor, cex=1.3<\/span>)<\/span><\/code><code>axis(1<\/span>)<\/span><\/code><code>dev.off()<\/span><\/code><code>}<\/span><\/code><code>############\u7ed8\u5236\u68ee\u6797\u56fe\u51fd\u6570############<\/span><\/span><\/code><code>#\u72ec\u7acb\u9884\u540e\u5206\u6790\uff0c\u8f93\u51fa\u8868\u683c<\/span><\/span><\/code><code>allOutTab=data.frame()<\/span><\/code><code>#\u521d\u59cb\u5316\u4e00\u4e2a\u7a7a\u7684\u6570\u636e\u6846 allOutTab\uff0c\u7528\u4e8e\u5b58\u50a8\u72ec\u7acb\u9884\u540e\u5206\u6790\u7684\u7ed3\u679c<\/span><\/span><\/code><code>sigGenes=c<\/span>(\"futime\"<\/span>,\"fustat\"<\/span>)<\/span><\/code><code>#\u4e00\u4e2a\u5b57\u7b26\u5411\u91cf sigGenes\uff0c\u5176\u4e2d\u5305\u542b\u521d\u59cb\u7684\u4e24\u4e2a\u5217\u540d \"futime\" \u548c \"fustat\"\uff0c\u8fd9\u4e9b\u5217\u7528\u4e8e\u6784\u5efa Cox \u6bd4\u4f8b\u98ce\u9669\u6a21\u578b\u3002<\/span><\/span><\/code><code>for<\/span>(i in<\/span> colnames(exp<\/span>[,3<\/span>:ncol(exp<\/span>)])){<\/span><\/code><code>#\u5faa\u73af\u904d\u5386\u8868\u8fbe\u6570\u636e\u7684\u5217\uff0c\u5176\u4e2d\u5305\u62ec\u5177\u4f53\u7684\u57fa\u56e0\u8868\u8fbe\u4fe1\u606f\u3002<\/span><\/span><\/code><code>#\u9488\u5bf9\u6bcf\u4e2a\u57fa\u56e0\uff0c\u6784\u5efa Cox \u6bd4\u4f8b\u98ce\u9669\u6a21\u578b\uff0c\u5e76\u5bf9\u6a21\u578b\u7684\u7ed3\u679c\u8fdb\u884c\u603b\u7ed3\uff08summary\uff09\u3002<\/span><\/span><\/code><code>rt=cbind(exp<\/span>[,1<\/span>:2<\/span>],cli,gene=exp<\/span>[,i])<\/span><\/code><code>colnames(rt)[ncol(rt)]=i<\/span><\/code><code>cox <- coxph(Surv(futime, fustat) ~ rt[,ncol(rt)], data = rt)<\/span><\/code><code>coxSummary = summary(cox)<\/span><\/code><code>outTab=data.frame()<\/span><\/code><code># p \u503c\u5c0f\u4e8e\u9884\u8bbe\u7684\u8fc7\u6ee4\u6761\u4ef6\uff08pFilter\uff09\uff0c\u5219\u7ee7\u7eed\u5728\u5185\u90e8\u5faa\u73af\u4e2d\uff0c\u5206\u522b\u6784\u5efa\u53ea\u5305\u542b\u4e00\u4e2a\u57fa\u56e0\u8868\u8fbe\u53d8\u91cf\u7684 Cox \u6bd4\u4f8b\u98ce\u9669\u6a21\u578b\u3002<\/span><\/span><\/code><code>if<\/span>(coxSummary$coefficients[,\"Pr(>|z|)\"<\/span>]<\/span><\/code><code>for<\/span>(j in<\/span> colnames(rt[,3<\/span>:ncol(rt)])){<\/span><\/code><code>coxJ <- coxph(Surv(futime, fustat) ~ rt[,j], data = rt)<\/span><\/code><code>coxSummaryJ = summary(coxJ)<\/span><\/code><code>coxP=coxSummaryJ$coefficients[,\"Pr(>|z|)\"<\/span>]<\/span><\/code><code>if<\/span>(coxSummaryJ$conf.int[,\"upper .95\"<\/span>] != Inf<\/span>){<\/span><\/code><code>outTab=rbind(outTab,<\/span><\/code><code>cbind(id=j,<\/span><\/code><code>HR=coxSummaryJ$conf.int[,\"exp(coef)\"<\/span>],<\/span><\/code><code>HR.95L=coxSummaryJ$conf.int[,\"lower .95\"<\/span>],<\/span><\/code><code>HR.95H=coxSummaryJ$conf.int[,\"upper .95\"<\/span>],<\/span><\/code><code>pvalue=coxSummaryJ$coefficients[,\"Pr(>|z|)\"<\/span>])<\/span><\/code><code>)<\/span><\/code><code>}<\/span><\/code><code>}<\/span><\/code><code>write.table(outTab,file=\"uniCox.txt\"<\/span>,sep=\"t\"<\/span>,row.names=F<\/span>,quote<\/span>=F<\/span>)<\/span><\/code><code>bioForest(coxFile=\"uniCox.txt\"<\/span>,forestFile=paste0(\"uni.\"<\/span>,i,\".pdf\"<\/span>),forestCol=\"green\"<\/span>)<\/span><\/code><code>unlink(\"uniCox.txt\"<\/span>)<\/span><\/code><code> <\/span><\/code><code>sigGenes=c<\/span>(sigGenes,i)<\/span><\/code><code>allOutTab=rbind(allOutTab,<\/span><\/code><code>cbind(id=i,<\/span><\/code><code>HR=coxSummary$conf.int[,\"exp(coef)\"<\/span>],<\/span><\/code><code>HR.95L=coxSummary$conf.int[,\"lower .95\"<\/span>],<\/span><\/code><code>HR.95H=coxSummary$conf.int[,\"upper .95\"<\/span>],<\/span><\/code><code>pvalue=coxSummary$coefficients[,\"Pr(>|z|)\"<\/span>])<\/span><\/code><code>)<\/span><\/code><code>}<\/span><\/code><code>}<\/span><\/code><code>#\u8f93\u51fa\u5355\u56e0\u7d20\u72ec\u7acb\u9884\u540e\u5206\u6790\u7ed3\u679c<\/span><\/span><\/code><code>write.table(allOutTab,file=\"uniIndep.xls\"<\/span>,sep=\"t\"<\/span>,row.names=F<\/span>,quote<\/span>=F<\/span>)<\/span><\/code><code>#\u8f93\u51fa\u5355\u56e0\u7d20\u72ec\u7acb\u9884\u540e\u57fa\u56e0\u8868\u8fbe\u91cf<\/span><\/span><\/code><code>indepSigExp=exp<\/span>[,sigGenes]<\/span><\/code><code>indepSigExp=cbind(id=row.names(indepSigExp),indepSigExp)<\/span><\/code><code>write.table(indepSigExp,file=\"uniIndepSigExp.txt\"<\/span>,sep=\"t\"<\/span>,row.names=F<\/span>,quote<\/span>=F<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.5142150803461063\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-08-26_\u300c\u8f6c\u300d\u7eaf\u4ee3\u7801\uff0c\u5e08\u59b9\u5e26\u4f60\u8f7b\u677e\u73a9\u8f6c\u751f\u5b58\u5206\u6790\u4e4b\u72ec\u7acb\u9884\u540e\u5206\u6790\/3_BkhxaR1ibD2xsWdEiaCYjJAiaB1x2w.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEX2ibTZqqt1FbZ0Xx0iclEKc3E1ic1Kn8F4Ow8DroVlGQVGE1qcpuBkhxaR1ibD2xsWdEiaCYjJAiaB1x2w\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"809\" style=\"vertical-align: middle;width: 100%;\" \/><\/section>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"2.239130434782609\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_mw5ic0n1lGIYQK8zfsHz4oicwtcsog.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEX2ibTZqqt1FbZ0Xx0iclEKc3lKWsWVOjG6W8fNHcXNly14y1OXmw5ic0n1lGIYQK8zfsHz4oicwtcsog\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"276\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.6136363636363636\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_jsfzwfOfJfRarEObaiaqdscoS92NUw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEX2ibTZqqt1FbZ0Xx0iclEKc3VcVY4EepWPLBgbXfiaXuGy7ibagjsfzwfOfJfRarEObaiaqdscoS92NUw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"660\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.6111951588502269\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-08-26_\u300c\u8f6c\u300d\u7eaf\u4ee3\u7801\uff0c\u5e08\u59b9\u5e26\u4f60\u8f7b\u677e\u73a9\u8f6c\u751f\u5b58\u5206\u6790\u4e4b\u72ec\u7acb\u9884\u540e\u5206\u6790\/6_dV6fhHicZkib7scAicnGdr5miaAa7A.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEX2ibTZqqt1FbZ0Xx0iclEKc3OaLjKMsNDUzSzFbXYb8K5nKJbySmdV6fhHicZkib7scAicnGdr5miaAa7A\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"661\" style=\"vertical-align: middle;width: 100%;\" \/><\/section>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.6196969696969697\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/7_dBLnol4uor9bK9wD4GkxaTbm5iazgg.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEX2ibTZqqt1FbZ0Xx0iclEKc3qRqMak4jsUqGPrriaiaT2OV7r8fdBLnol4uor9bK9wD4GkxaTbm5iazgg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"660\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section powered-by=\"xiumi.us\">\n\u5c06\u72ec\u7acb\u9884\u540e\u5206\u6790\u7684\u7ed3\u679c\u5199\u5165\u540d\u4e3a “uniIndep.xls” \u7684\u6587\u4ef6\u4e2d\uff0c\u5176\u4e2d\u5305\u62ec\u6bcf\u4e2a\u57fa\u56e0\u7684Hazard Ratio\u3001\u7f6e\u4fe1\u533a\u95f4\u548cp\u503c\u7b49\u4fe1\u606f\u3002\u6b64\u5916\uff0c\u4ee3\u7801\u8fd8\u5c06\u6ee1\u8db3\u663e\u8457\u6027\u6761\u4ef6\u7684\u57fa\u56e0\u7684\u8868\u8fbe\u6570\u636e\u5199\u5165\u540d\u4e3a “uniIndepSigExp.txt” \u7684\u6587\u4ef6\u4e2d\u3002<\/p>\n <\/p>\n\u901a\u8fc7\u751f\u5b58\u5206\u6790\u548c\u72ec\u7acb\u9884\u540e\u5206\u6790\uff0c\u53ef\u4ee5\u8bc6\u522b\u51fa\u5728\u751f\u5b58\u7387\u65b9\u9762\u5177\u6709\u663e\u8457\u5f71\u54cd\u7684\u57fa\u56e0\u3002\u8fd9\u4e9b\u57fa\u56e0\u53ef\u80fd\u5728\u75be\u75c5\u8fdb\u7a0b\u3001\u6cbb\u7597\u53cd\u5e94\u7b49\u65b9\u9762\u8d77\u7740\u91cd\u8981\u4f5c\u7528\u3002\u53ef\u4ee5\u8fdb\u4e00\u6b65\u5206\u6790\u8fd9\u4e9b\u57fa\u56e0\u7684\u529f\u80fd\u3001\u901a\u8def\u4ee5\u53ca\u4e0e\u75be\u75c5\u76f8\u5173\u7684\u673a\u5236\uff0c\u4e0b\u671f\u5c06\u4e3a\u4f60\u5e26\u6765\u66f4\u591aR\u8bed\u8a00\u7684\u9a9a\u64cd\u4f5c\u6280\u5de7\uff0c\u4ee5\u4e0b\u63a8\u8350\u7684\u662f\u4e00\u4e2a\u591a\u529f\u80fd\u7684\u751f\u4fe1\u5e73\u53f0\u3002<\/p>\n<\/section>\n<section powered-by=\"xiumi.us\">\n\u4e91\u751f\u4fe1\u5e73\u53f0\u94fe\u63a5\uff1a<\/p>\nhttp:\/\/www.biocloudservice.com\/home.html\u3002<\/p>\n\u4e91\u751f\u4fe1\u5e73\u53f0\u94fe\u63a5\uff1a<\/p>\nhttp:\/\/www.biocloudservice.com\/home.html\u3002<\/p>\n<\/section>\n<section style=\"text-align: center;justify-content: center;display: flex;flex-flow: row nowrap;margin-top: 10px;margin-bottom: 5px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: top;width: auto;align-self: flex-start;flex: 0 0 auto;min-width: 5%;height: auto;\">\n<section style=\"margin-top: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;width: 19px;height: auto;\"><img decoding=\"async\" data-ratio=\"0.8379629629629629\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-08-26_\u300c\u8f6c\u300d\u7eaf\u4ee3\u7801\uff0c\u5e08\u59b9\u5e26\u4f60\u8f7b\u677e\u73a9\u8f6c\u751f\u5b58\u5206\u6790\u4e4b\u72ec\u7acb\u9884\u540e\u5206\u6790\/8_t4k8iazF0KYgbhpAicSMw4E1OYB89A.png\" onerror=\"this.src='\u56fe\u7247\/\u751f\u4fe1\u679c_2023-08-26_\u300c\u8f6c\u300d\u7eaf\u4ee3\u7801\uff0c\u5e08\u59b9\u5e26\u4f60\u8f7b\u677e\u73a9\u8f6c\u751f\u5b58\u5206\u6790\u4e4b\u72ec\u7acb\u9884\u540e\u5206\u6790\/9_t4k8iazF0KYgbhpAicSMw4E1OYB89A.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEX2ibTZqqt1FbZ0Xx0iclEKc3UFPibcicFgrwMjzs1QozV1aZAwgNt4k8iazF0KYgbhpAicSMw4E1OYB89A\/640?wx_fmt=png''\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" \/><\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: auto;align-self: flex-start;flex: 0 0 auto;min-width: 5%;height: auto;\">\n<section style=\"margin-top: -9px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;width: 11.4844px;height: auto;\"><img decoding=\"async\" data-ratio=\"0.8379629629629629\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-08-26_\u300c\u8f6c\u300d\u7eaf\u4ee3\u7801\uff0c\u5e08\u59b9\u5e26\u4f60\u8f7b\u677e\u73a9\u8f6c\u751f\u5b58\u5206\u6790\u4e4b\u72ec\u7acb\u9884\u540e\u5206\u6790\/8_t4k8iazF0KYgbhpAicSMw4E1OYB89A.png\" onerror=\"this.src='\u56fe\u7247\/\u751f\u4fe1\u679c_2023-08-26_\u300c\u8f6c\u300d\u7eaf\u4ee3\u7801\uff0c\u5e08\u59b9\u5e26\u4f60\u8f7b\u677e\u73a9\u8f6c\u751f\u5b58\u5206\u6790\u4e4b\u72ec\u7acb\u9884\u540e\u5206\u6790\/9_t4k8iazF0KYgbhpAicSMw4E1OYB89A.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEX2ibTZqqt1FbZ0Xx0iclEKc3UFPibcicFgrwMjzs1QozV1aZAwgNt4k8iazF0KYgbhpAicSMw4E1OYB89A\/640?wx_fmt=png''\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" \/><\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"text-align: center;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"font-size: 24px;color: rgb(249, 172, 172);\">\nEND<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.3488888888888889\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/10_BoDuficWb7YjnP0CXo0mIcibhsXn8w-3.jpg?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_jpg\/oCSOtP61aEUlxqHhbZryhECGXicgBrLn1ZkgkpYia2qsgSgNWPQMp0RiaIAmlBoDuficWb7YjnP0CXo0mIcibhsXn8w\/640?wx_fmt=jpeg'\" data-type=\"jpeg\" data-w=\"900\" style=\"\" data-recalc-dims=\"1\" \/><\/p>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.5555555555555556\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/11_akXKU5NcO1KwuWc1Rk7ZJ56LC2pYrQ-7.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEXjjmsEC5aXz0RE4be2ib1fJPnBD8yX0Z6OF2zocd2ngHpLOakXKU5NcO1KwuWc1Rk7ZJ56LC2pYrQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"900\" style=\"\" data-recalc-dims=\"1\" \/><\/p>\n<mp-style-type data-value=\"3\"><\/mp-style-type><\/p>\n<div class=\"msg_source_url\"><a href=\"http:\/\/www.biocloudservice.com\/home.html\" target=\"_blank\" rel=\"noopener\">\u9605\u8bfb\u539f\u6587<\/a><\/div>\n<\/content><\/p>\n<div class=\"msg_source_url\"><a href=\"http:\/\/www.biocloudservice.com\/home.html\" target=\"_blank\" rel=\"noopener\">\u9605\u8bfb\u539f\u6587<\/a><\/div>\n<\/div>\n<\/body> \n<\/html><\/p>\n","protected":false},"excerpt":{"rendered":"\u7eaf\u4ee3\u7801\uff0c\u5e08\u59b9\u5e26\u4f60\u8f7b\u677e\u73a9\u8f6c\u751f\u5b58\u5206\u6790\u4e4b\u72ec\u7acb\u9884\u540e\u5206\u6790 \u5c0f\u5e08\u59b9 \u751f\u4fe1\u679c 2 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