{"id":24932,"date":"2024-01-17T16:53:41","date_gmt":"2024-01-17T08:53:41","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=24932"},"modified":"2024-01-17T16:53:44","modified_gmt":"2024-01-17T08:53:44","slug":"%e5%b9%b2%e8%b4%a7%e6%89%b9%e9%87%8f%e5%a4%84%e7%90%86%e6%b3%9b%e7%99%8c%e7%9b%b8%e5%85%b3%e7%94%9f%e5%ad%98km%e5%88%86%e6%9e%90%e7%bb%98%e5%9b%be","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=24932","title":{"rendered":"\u5e72\u8d27\u6279\u91cf\u5904\u7406\u6cdb\u764c\u76f8\u5173\u751f\u5b58KM\u5206\u6790\u7ed8\u56fe"},"content":{"rendered":"

\u751f\u5b58\u5206\u6790\u4e2d\u7684Kaplan-Meier\u66f2\u7ebf\uff08\u4e5f\u79f0\u4e3aKM\u66f2\u7ebf\uff09\u662f\u4e00\u79cd\u5e38\u7528\u7684\u7edf\u8ba1\u65b9\u6cd5\uff0c\u7528\u4e8e\u4f30\u8ba1\u4e0d\u540c\u7ec4\u522b\u4e4b\u95f4\u7684\u751f\u5b58\u51fd\u6570\u5dee\u5f02\u3002KM\u66f2\u7ebf\u663e\u793a\u4e86\u5728\u7ed9\u5b9a\u65f6\u95f4\u8303\u56f4\u5185\u751f\u5b58\u4e0b\u6765\u7684\u60a3\u8005\u6bd4\u4f8b\u968f\u65f6\u95f4\u7684\u53d8\u5316\u60c5\u51b5\u3002<\/p>\n

KM\u66f2\u7ebf\u901a\u5e38\u7528\u4e8e\u4ee5\u4e0b\u60c5\u51b5\uff1a \u6bd4\u8f83\u4e0d\u540c\u6cbb\u7597\u7ec4\u6216\u6cbb\u7597\u65b9\u6848\u7684\u751f\u5b58\u5dee\u5f02\uff1a\u4f8b\u5982\uff0c\u5bf9\u4e8e\u67d0\u79cd\u764c\u75c7\uff0c\u53ef\u4ee5\u5c06\u60a3\u8005\u5206\u4e3a\u63a5\u53d7\u4e0d\u540c\u6cbb\u7597\u65b9\u6848\u7684\u7ec4\uff0c\u5e76\u6bd4\u8f83\u5404\u7ec4\u7684\u751f\u5b58\u60c5\u51b5\u3002 \u8bc4\u4f30\u9884\u540e\u56e0\u7d20\u5bf9\u751f\u5b58\u7684\u5f71\u54cd\uff1a\u4f8b\u5982\uff0c\u7814\u7a76\u7279\u5b9a\u57fa\u56e0\u53d8\u5f02\u4e0e\u60a3\u8005\u751f\u5b58\u4e4b\u95f4\u7684\u5173\u7cfb\uff0c\u6216\u8005\u8bc4\u4f30\u5176\u4ed6\u4e34\u5e8a\u7279\u5f81\uff08\u5982\u5e74\u9f84\u3001\u6027\u522b\u3001\u80bf\u7624\u5206\u671f\u7b49\uff09\u5bf9\u751f\u5b58\u7684\u5f71\u54cd\u3002<\/p>\n

\u7ed8\u5236KM\u66f2\u7ebf\u7684\u6b65\u9aa4\u5982\u4e0b\uff1a \u6536\u96c6\u751f\u5b58\u6570\u636e\uff1a\u5305\u62ec\u6bcf\u4e2a\u4e2a\u4f53\u7684\u751f\u5b58\u65f6\u95f4\u548c\u4e8b\u4ef6\u72b6\u6001\uff08\u5982\u751f\u5b58\u6216\u6b7b\u4ea1\uff09\u3002\u6839\u636e\u7814\u7a76\u76ee\u7684\u548c\u53d8\u91cf\u7279\u5f81\uff0c\u5c06\u4e2a\u4f53\u5206\u4e3a\u4e0d\u540c\u7684\u7ec4\u522b\uff08\u4f8b\u5982\u6cbb\u7597\u7ec4\u548c\u5bf9\u7167\u7ec4\uff09\u3002\u4f7f\u7528Kaplan-Meier\u65b9\u6cd5\u8ba1\u7b97\u6bcf\u4e2a\u7ec4\u522b\u4e2d\u5728\u7ed9\u5b9a\u65f6\u95f4\u70b9\u751f\u5b58\u4e0b\u6765\u7684\u60a3\u8005\u6bd4\u4f8b\u3002\u7ed8\u5236KM\u66f2\u7ebf\uff1a\u5c06\u4e0d\u540c\u7ec4\u522b\u5728\u7ed9\u5b9a\u65f6\u95f4\u70b9\u7684\u751f\u5b58\u6bd4\u4f8b\u7ed8\u5236\u5728\u540c\u4e00\u5f20\u56fe\u4e0a\u3002\u8fdb\u884c\u7edf\u8ba1\u68c0\u9a8c\uff1a\u4f7f\u7528log-rank\u68c0\u9a8c\u6216\u5176\u4ed6\u5408\u9002\u7684\u65b9\u6cd5\u6bd4\u8f83\u4e0d\u540c\u7ec4\u522b\u4e4b\u95f4\u7684\u751f\u5b58\u5dee\u5f02\u3002<\/p>\n

library(limma)<\/p>\n

library(survival)<\/p>\n

library(survminer)<\/p>\n

library(data.table)<\/p>\n

library(tidyverse)<\/p>\n

library(ggsignif)<\/p>\n

library(RColorBrewer)<\/p>\n

#\u9996\u5148\uff0c\u52a0\u8f7d\u4e86\u4e00\u7cfb\u5217\u6240\u9700\u7684R\u5305<\/p>\n

files=dir(“.\/DFI\/”)<\/p>\n

\u901a\u8fc7dir(“.\/DFI\/”)\u83b7\u53d6”.\/DFI\/”\u76ee\u5f55\u4e0b\u7684\u6587\u4ef6\u5217\u8868\uff0c\u8fd9\u4e9b\u6587\u4ef6\u5305\u542b\u4e86\u6bcf\u79cd\u764c\u75c7\u7c7b\u578b\u7684\u751f\u5b58\u6570\u636e\u3002<\/p>\n

pFilter=1 #pvalue ALL DATA,NO filter<\/p>\n

#if(pValue<pFilter){<\/p>\n

# if(pValue<0.001){<\/p>\n

# pValue=”p<0.001″<\/p>\n

# }else{<\/p>\n

# pValue=paste0(“p=”,sprintf(“%.03f”,pValue))<\/p>\n

#}<\/p>\n

#for tumour types<\/p>\n

#\u901a\u8fc7\u4e00\u4e2a\u5faa\u73af\u904d\u5386\u6bcf\u4e2a\u6587\u4ef6\u8fdb\u884c\u5904\u7406\u3002\u5728\u5faa\u73af\u4e2d\uff0c\u9996\u5148\u8bfb\u53d6\u6587\u4ef6\u5185\u5bb9\u5e76\u8f6c\u6362\u4e3a<\/p>\n

#\u6570\u636e\u6846\u3002\u7136\u540e\u5bf9\u6570\u636e\u6846\u8fdb\u884c\u5904\u7406\uff0c\u8c03\u6574\u5217\u540d\u548c\u6570\u636e\u683c\u5f0f\u3002\u5c06\u5b58\u6d3b\u65f6\u95f4\uff08futime\uff09#\u4ece\u5929\u8f6c\u6362\u4e3a\u5e74\uff0c\u5c06tpm\u8f6c\u6362\u4e3a\u6570\u503c\u578b\u6570\u636e\u3002<\/p>\n

for ( i in 1:length(files) ){<\/p>\n

dirname=files[i]<\/p>\n

rt=fread(paste0(“.\/DFI\/”,dirname),header=T,check.names=F)<\/p>\n

rt=as.data.frame.matrix(rt)<\/p>\n

<\/p>\n

#rownames(rt)=rt[,1]<\/p>\n

rt=rt[,-1]<\/p>\n

rt=na.omit(rt)<\/p>\n

colnames(rt)[1:2]=c(“fustat”,”futime”)<\/p>\n

b=rt[,2]<\/p>\n

rt=cbind(b,rt)<\/p>\n

rt=rt[,-3]<\/p>\n

colnames(rt)[1]=”futime”<\/p>\n

<\/p>\n

rt$futime=rt$futime\/365 #Survival time in years<\/p>\n

rt$tpm=as.numeric(rt$tpm)<\/p>\n

#rt$tissue=as.factor(rt$tissue)<\/p>\n

<\/p>\n

#######files names<\/p>\n

tmp<- strsplit(dirname,split=”.”,fixed=TRUE)<\/p>\n

dirnam<-unlist(lapply(tmp,head,1))<\/p>\n

tissue=c(“ACC”, “BLCA”, “BRCA”, “CESC”, “CHOL”, “COAD”, “DLBC”, “ESCA”, “GBM”, “HNSC”, “KICH”, “KIRC”, “KIRP”, “LGG”, “LIHC”, “LUAD”, “LUSC”, “MESO”, “OV”, “PAAD”, “PCPG”, “PRAD”, “READ”, “SARC”, “SKCM”, “STAD”, “TGCT”, “THCA”, “THYM”, “UCEC”, “UCS”, “UVM”)<\/p>\n

for ( j in 1:length(tissue) ){<\/p>\n

#for(i in levels(rt[,”tissue”] )){<\/p>\n

id=rt[1,6]<\/p>\n

cancer=tissue[j]<\/p>\n

rt1=rt[(rt$tissue %in% cancer),] # by tumour type<\/p>\n

group=ifelse(rt1[,”tpm”]>median(rt1[,”tpm”]),”high”,”low”)<\/p>\n

#\u6839\u636e\u764c\u75c7\u7c7b\u578b\u8fdb\u884c\u5b50\u96c6\u9009\u62e9\uff0c\u5f97\u5230\u7279\u5b9a\u764c\u75c7\u7c7b\u578b\u7684\u6570\u636e\u6846\uff08rt1\uff09\u3002\u7136\u540e\u6839\u636etpm\u7684\u4e2d\u4f4d\u6570\u5c06\u6837\u672c\u5206\u4e3a\u9ad8\u8868\u8fbe\u7ec4\u548c\u4f4e\u8868\u8fbe\u7ec4\uff0c\u521b\u5efa\u4e00\u4e2a\u65b0\u7684\u5217group\u3002\u901a\u8fc7\u5224\u65ad\u662f\u5426\u540c\u65f6\u5305\u542bTRUE\u548cFALSE\u6765\u6392\u9664\u8868\u8fbe\u6c34\u5e73\u76f8\u540c\u7684\u6837\u672c\u7ec4\u3002<\/p>\n

<\/p>\n

a=rt1[,”tpm”]>median(rt1[,”tpm”])<\/p>\n

#\u5982\u679c\u6ee1\u8db3\u6761\u4ef6\uff0c\u63a5\u4e0b\u6765\u8fdb\u884c\u751f\u5b58\u5206\u6790\u3002\u9996\u5148\u4f7f\u7528survdiff\u51fd\u6570\u8fdb\u884c\u7ec4\u95f4\u751f\u5b58\u5dee\u5f02\u7684\u7edf\u8ba1\u68c0\u9a8c\uff0c\u5e76\u8ba1\u7b97p\u503c\u3002\u7136\u540e\u4f7f\u7528survfit\u51fd\u6570\u62df\u5408\u751f\u5b58\u66f2\u7ebf\u3002<\/p>\n

if(length(table(group))==1) {next}<\/p>\n

if(TRUE & FALSE %in% a){<\/p>\n

diff=survdiff(Surv(futime,fustat)~ group,data = rt1) #Survival of rt1 data by groups<\/p>\n

pValue=1-pchisq(diff$chisq,df=1) #test<\/p>\n

fit <- survfit(Surv(futime,fustat) ~ group, data = rt1)<\/p>\n

#KM survival curves<\/p>\n

#\u63a5\u4e0b\u6765\uff0c\u4f7f\u7528ggsurvplot\u51fd\u6570\u751f\u6210\u751f\u5b58\u66f2\u7ebf\u56fe\u3002\u8fd9\u91cc\u8bbe\u7f6e\u4e86\u56fe\u5f62\u7684\u6807\u9898\u3001p\u503c\u663e\u793a\u3001\u56fe\u4f8b\u3001\u5750\u6807\u8f74\u6807\u7b7e\u7b49\u53c2\u6570\uff0c\u5e76\u4f7f\u7528\u4e0d\u540c\u7684\u989c\u8272\u8868\u793a\u9ad8\u8868\u8fbe\u7ec4\u548c\u4f4e\u8868\u8fbe\u7ec4\u3002<\/p>\n

#\u6700\u540e\uff0c\u5c06\u751f\u6210\u7684\u751f\u5b58\u66f2\u7ebf\u56fe\u4fdd\u5b58\u4e3aPDF\u6587\u4ef6\uff0c\u547d\u540d\u65b9\u5f0f\u4e3a”\u6587\u4ef6\u540d_\u764c\u75c7\u7c7b\u578b_p\u503c_sur_DFI.pdf”\u3002<\/p>\n

surPlot=ggsurvplot(fit,<\/p>\n

data=rt1,<\/p>\n

title=paste0(“Cancer: “,cancer=tissue[j]),<\/p>\n

pval=pValue,<\/p>\n

pval.size=6,<\/p>\n

legend.labs=c(“high”,”low”),<\/p>\n

legend.title=paste0(id,” levels”),<\/p>\n

font.legend=12,<\/p>\n

xlab=”Time(years)”,<\/p>\n

ylab=”Overall survival”,<\/p>\n

break.time.by = 1,<\/p>\n

palette=c(“red”,”blue”),<\/p>\n

conf.int=F,<\/p>\n

fontsize=4,<\/p>\n

risk.table=TRUE,<\/p>\n

risk.table.title=””,<\/p>\n

risk.table.height=.25)<\/p>\n

pdf(paste0(“.\/picture_DFI\/”,dirnam,”_”,cancer=tissue[j],”_”,pValue, “_sur_DFI.pdf”),width = 10, height = 7.5)<\/p>\n

#ggsave(paste0(“.\/picture_expTime_TG_GTEX\/”,dirnam,”_”,cancer=tissue[j],”_”,pValue, “_sur_os.svg”), width = 14, height = 15)<\/p>\n

print(surPlot)<\/p>\n

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

}<\/p>\n

}<\/p>\n

}<\/p>\n

#####<\/p>\n

KM\u66f2\u7ebf\u56fe\u901a\u5e38\u5305\u62ec\u4ee5\u4e0b\u4fe1\u606f\uff1a \u65f6\u95f4\u8f74\uff1a\u8868\u793a\u89c2\u5bdf\u65f6\u95f4\u7684\u6a2a\u8f74\uff0c\u901a\u5e38\u4ee5\u5e74\u3001\u6708\u3001\u5468\u7b49\u4e3a\u5355\u4f4d\u3002 \u751f\u5b58\u7387\u8f74\uff1a\u8868\u793a\u751f\u5b58\u60a3\u8005\u7684\u6bd4\u4f8b\uff0c\u7eb5\u8f74\u8303\u56f4\u4ece0\u52301\u3002\u66f2\u7ebf\uff1a\u6bcf\u4e2a\u7ec4\u522b\u7684\u751f\u5b58\u66f2\u7ebf\uff0c\u4ee5\u5b9e\u7ebf\u6216\u865a\u7ebf\u8868\u793a\u3002 \u6807\u9898\u548c\u56fe\u4f8b\uff1a\u7528\u4e8e\u6807\u8bc6\u66f2\u7ebf\u5bf9\u5e94\u7684\u7ec4\u522b\u548c\u5176\u4ed6\u91cd\u8981\u4fe1\u606f\u3002<\/p>\n

\u901a\u8fc7\u7ed8\u5236KM\u66f2\u7ebf\uff0c\u53ef\u4ee5\u76f4\u89c2\u5730\u6bd4\u8f83\u4e0d\u540c\u7ec4\u522b\u4e4b\u95f4\u7684\u751f\u5b58\u5dee\u5f02\uff0c\u5e2e\u52a9\u7814\u7a76\u4eba\u5458\u548c\u4e34\u5e8a\u533b\u751f\u4e86\u89e3\u67d0\u79cd\u56e0\u7d20\u5bf9\u751f\u5b58\u7684\u5f71\u54cd\uff0c\u4ee5\u6307\u5bfc\u6cbb\u7597\u51b3\u7b56\u548c\u9884\u540e\u8bc4\u4f30\u3002\u6709\u95ee\u9898\u53ef\u4ee5\u8054\u7cfb\u5c0f\u679c\u3002<\/p>\n

\u6765\u7ed9\u5927\u5bb6\u5c55\u793a\u5c55\u793a\u7ed3\u679c\u56fe\u5427\uff0c\u4f7f\u7528firefox\u547d\u4ee4\u3002<\/p>\n

<\/p>\n

\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

\u4e91\u751f\u4fe1\u5e73\u53f0\u94fe\u63a5\uff1ahttp:\/\/www.biocloudservice.com\/home.html\u3002<\/a><\/p>\n

\u4e91\u751f\u4fe1\u5e73\u53f0\u94fe\u63a5\uff1ahttp:\/\/www.biocloudservice.com\/home.html\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"

\u751f\u5b58\u5206\u6790\u4e2d\u7684Kaplan-Meier\u66f2\u7ebf\uff08\u4e5f\u79f0\u4e3aKM\u66f2\u7ebf\uff09\u662f\u4e00\u79cd\u5e38\u7528\u7684\u7edf\u8ba1\u65b9\u6cd5\uff0c\u7528\u4e8e\u4f30\u8ba1\u4e0d\u540c\u7ec4\u522b\u4e4b\u95f4\u7684\u751f\u5b58\u51fd\u6570 […]<\/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\/24932"}],"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=24932"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/24932\/revisions"}],"predecessor-version":[{"id":24939,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/24932\/revisions\/24939"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=24932"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=24932"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=24932"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}