我在运行一段代码的时候出现了这样的错误:Error in if (coxP < pFilter) { : missing value where TRUE/FALSE needed.
library(survival)
pFilter=0.05 #显著性过滤标准
setwd("E://Bioinformation//TCGA-Impro//TCGA-OV//ZX-GTEx-TCGA") #设置工作目录
rt=read.table("expTime.txt",header=T,sep="\t",check.names=F,row.names=1) #读取输入文件
outTab=data.frame()
sigGenes=c("futime","fustat")
for(i in colnames(rt[,3:ncol(rt)])){
cox <- coxph(Surv(futime, fustat) ~ rt[,i], data = rt)
coxSummary = summary(cox)
coxP = coxSummary$coefficients[,"Pr(>|z|)"]
if(coxP<pFilter){
sigGenes = c(sigGenes,i)
outTab = rbind(outTab,
cbind(id = i,
HR = coxSummary$conf.int[,"exp(coef)"],
HR.95L = coxSummary$conf.int[,"lower .95"],
HR.95H = coxSummary$conf.int[,"upper .95"],
pvalue = coxSummary$coefficients[,"Pr(>|z|)"])
)
}
}
write.table(outTab,file="uniCox.txt",sep="\t",row.names=F,quote=F)
uniSigExp = rt[,sigGenes]
uniSigExp = cbind(id=row.names(uniSigExp),uniSigExp)
write.table(uniSigExp,file="uniSigExp.txt",sep="\t",row.names=F,quote=F)`
数据好像无法上传呢?