BraunSurvivalAnalysis.Rmd

---
title: "BraunSurvivalModel"
output: html_document
editor_options: 
  chunk_output_type: console
---

```{r}
clinicalData = readxl::read_xlsx("D:/FertigLabLargeData/Network_Cancer/Braun2020/41591_2020_839_MOESM2_ESM.xlsx", sheet = 1, skip = 1)

clinicalData$Age = as.numeric(clinicalData$Age)
#remove NA age
clinicalDataSub = clinicalData[-which(is.na(clinicalData$Age)),]

hist(clinicalDataSub$Age)

#cox model for PFS
library(survival)
coxUni = coxph(Surv(PFS,PFS_CNSR)~Age, clinicalDataSub)
coxUni

#for OS
coxUniOS = coxph(Surv(OS,OS_CNSR)~Age, clinicalDataSub)
coxUniOS

#multivariate model
clinicalDataSub$Sex[which(clinicalDataSub$Sex %in% c("Female", "FEMALE"))] = "F"
clinicalDataSub$Sex[which(clinicalDataSub$Sex %in% c("Male", "MALE"))] = "M"

clinicalDataSub$Number_of_Prior_Therapies = as.numeric(clinicalDataSub$Number_of_Prior_Therapies)



coxMVar = coxph(Surv(PFS,PFS_CNSR)~Age + Sex + Number_of_Prior_Therapies + Tumor_Sample_Primary_or_Metastasis, clinicalDataSub)
summary(coxMVar)
write.csv(summary(coxMVar)$coefficients, "Data/coxPFS_Braun.csv")

coxMVarOS = coxph(Surv(OS,OS_CNSR)~Age + Sex + Number_of_Prior_Therapies + Tumor_Sample_Primary_or_Metastasis, clinicalDataSub)
summary(coxMVarOS)
write.csv(summary(coxMVarOS)$coefficients, "Data/coxOS_Braun.csv")


#KM curve
clinicalDataSub$AgeGroup = cut(clinicalDataSub$Age, c(20,65,90), labels = c("65Under", "Over65"))

library(survminer)

kmFit <- survfit(Surv(PFS,PFS_CNSR)~AgeGroup, data = clinicalDataSub)

ggsurvplot(kmFit, risk.table = T, pval = F, conf.int = T, xlim = c(0, 70))

#for OS
kmFitOS <- survfit(Surv(OS,OS_CNSR)~AgeGroup, data = clinicalDataSub)

ggsurvplot(kmFitOS, risk.table = T, pval = F, conf.int = T, xlim = c(0, 72))
```