代码:
library(survival)
library(survminer)
coxPfilter=0.05
inputFile="TCGA.expTime.txt"
setwd("D:/01/16.uniCox")
rt=read.table(inputFile, header=T, sep="\t", check.names=F, row.names=1)
rt$futime=rt$futime/365
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$coefficients[,"Pr(>|z|)"]
if(coxP<coxPfilter){
sigGenes=c(sigGenes,i)
outTab=rbind(outTab,
cbind(id=i,
HR=coxSummary$conf.int[,"exp(coef)"],
HR.95L=coxSummary$conf.int[,"lower .95"],
HR.95H=coxSummary$conf.int[,"upper .95"],
pvalue=coxSummary$coefficients[,"Pr(>|z|)"])
)
}
}
报错:
Warning messages: 1: In coxph.fit(X, Y, istrat, offset, init, control, weights = weights, : Loglik converged before variable 1 ; coefficient may be infinite. 2: In coxph.fit(X, Y, istrat, offset, init, control, weights = weights, : Loglik converged before variable 1 ; coefficient may be infinite. 3: In coxph.fit(X, Y, istrat, offset, init, control, weights = weights, : Loglik converged before variable 1 ; coefficient may be infinite. ...
即:在 coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Loglik 收敛于变量 1 之前;系数可以是无限的。
数据不大,数据处理时已标准化,且没有空缺值,但是不知道怎么改,求大佬指点。