setwd('D:/brca')

library('plyr')

library("ipred")

library("survival")

library("survivalROC")

library("glmnet")

kx=read.csv("brca_cox.csv",row.names= 1)

mysurv=Surv(kx$time,kx$status)

Unicox <- function(x){

  #cat("aa:",x,"\n")

  fml <- as.formula(paste0('mysurv~', x))

  gcox <- coxph(fml, kx)

  cox_sum <- summary(gcox)

  HR <- round(cox_sum$coefficients[,2],2)

  PValue <- round(cox_sum$coefficients[,5],4)

  CI <- paste0(round(cox_sum$conf.int[,3:4],2),collapse='-')

  Uni_cox <- data.frame('Characteristics' = x,

                        'Hazard Ratio' = HR,

                        'CI95' = CI,

                        'P value' = PValue)

  return(Uni_cox)

}

VarNames <-colnames(kx)[3:ncol(kx)]

Univar <- lapply(VarNames, Unicox)

Univar <- ldply(Univar, data.frame)

Univar[,5]=p.adjust(Univar$P.value, method ="fdr", n=dim(Univar)[1])#

colnames(Univar)<-c("Characteristics", "Hazard.Ratio", "CI95", "P.value", "adj.p")

dd=matrix(0,1,ncol(kx))

dd[1,3:ncol(kx)]=Univar$P.value

dd=data.frame(dd)

colnames(dd)=colnames(kx)

ee=rbind(dd,kx)

ff=ee[,ee[1,]<0.05]

gg=ee[,ee[1,]<0.01]

cox2=ff[-1,]

write.csv(cox2,'brca_cox2.csv')