示例：

 

sample	hsa-miR-339-5p	hsa-miR-324-5p	Event	months
TCGA-NJ-A4YP	5.37649676	4.57839941	Alive	1.64
TCGA-86-8278	4.340845007	3.698656714	Alive	31.01
TCGA-62-A470	5.55662622	5.913658335	Dead	39.22
TCGA-44-6778	4.76629652	2.877071024	Alive	61.24
TCGA-49-AARQ	6.90221694	5.896734003	Alive	221.16
TCGA-97-A4M1	5.5758414	4.864950886	Alive	19.74
TCGA-99-8033	5.773618233	5.035791207	Dead	21.55
TCGA-78-7149	3.56912225	4.834641484	Alive	129.43
TCGA-50-6597	5.207816378	3.943285313	Dead	41.66
TCGA-69-8255	5.138845111	4.745133898	Alive	4.24

rm(list = ls())

setwd(“D:/”)

library(readxl)

library(survival)

library(plyr)

LUAD<-read_xlsx(“LUAD2.xlsx”)

attach(LUAD)

#单因素COX

#无NA

my.surv <- Surv(`months` ,Event==”Dead”)

m=coxph(my.surv~`hsa-miR-148a-3p`,data = LUAD)

sm<-summary(m)

HR <- round(sm$coefficients[,2],3)

HRCILL <- round(sm$conf.int[,3],3)

HRCIUL <- round(sm$conf.int[,4],3)

pValue <- round(sm$coefficients[,5],3)

tmp <- data.frame(“miRNAs” = colnames(LUAD0)[2],

 “N”= nrow(LUAD0),

 “pValue” = pValue,

 “HR” = HR,

 “HRCILL” = HRCILL,

 “HRCIUL” = HRCIUL)

unicox<-function(x){

 FML <- as.formula(paste0(“my.surv~”,x))

 m=coxph(FML,data = LUAD)

 sm<-summary(m)

 HR <- round(sm$coefficients[,2],3)

 HRCILL <- round(sm$conf.int[,3],3)

 HRCIUL <- round(sm$conf.int[,4],3)

 pValue <- round(sm$coefficients[,5],3)

 tmp <- data.frame(“miRNAs” = colnames(LUAD0)[2],

“N”= nrow(LUAD0),

“pValue” = pValue,

“HR” = HR,

“HRCILL” = HRCILL,

“HRCIUL” = HRCIUL)

 return(tmp)

}

varNames <- colnames(LUAD)[c(2:200)]

univar <- lapply(varNames, unicox)

univar <- ldply(univar,data.frame)

#有NA

unicox<-function(x){

 LUAD0 <- LUAD[,c(1,x,201,202)]

 LUAD0 <- na.omit(LUAD0)

 if(length(which((LUAD0[,3]==”Dead”)))<20)

{

return()

} else {

 my.surv <- Surv(LUAD0$months ,LUAD0$Event==”Dead”)

 FML <- as.formula(paste0(“my.surv~”,colnames(LUAD0)[2]))

 m=coxph(FML,data = LUAD0)

 sm<-summary(m)

 HR <- round(sm$coefficients[,2],3)

 HRCILL <- round(sm$conf.int[,3],3)

 HRCIUL <- round(sm$conf.int[,4],3)

 pValue <- round(sm$coefficients[,5],3)

 tmp <- data.frame(“miRNAs” = colnames(LUAD0)[2],

“N”= nrow(LUAD0),

“pValue” = pValue,

“HR” = HR,

“HRCILL” = HRCILL,

“HRCIUL” = HRCIUL)

 return(tmp)

}

}

univar <- lapply(c(2:200), unicox)

univar <- ldply(univar, data.frame)

View(univar)

sigCOX <- univar[which(univar[,3]<0.05),]

sigCOX <- sigCOX[order(sigCOX$pValue,decreasing = F),]

#多因素Cox

attach(LUAD)

my.surv <- Surv(`months` ,Event==”Dead”)

multicox <- oxph(my.surv~hsa_miR_148a_3p+hsa_miR_6715b_3p+hsa_miR_133b+hsa_miR_148a_5p+hsa_miR_199b_5p+hsa_miR_145_3p+hsa_miR_133a_3p+hsa_let_7c_5p+hsa_miR_195_5p+hsa_miR_30a_5p,data = LUAD)

multisum <- summary(multicox)

MHR <- round(multisum$coefficients[,2],3)

MPV <- round(multisum$coefficients[,5],3)

MCIL <- round(multisum$conf.int[,3],3)

MCIU <- round(multisum$conf.int[,4],3)

multicox <- data.frame(“pValue” = MPV,

  “HR” = MHR,

  “MCIL” = MCIL,

  “MCIU” = MCIU)