brca/SUBTYPE1.R at main · schwinge/brca · GitHub

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library(survival)
library(survminer)
m<-read.table("metaunicox")
s<-read.table("scmod2subtype")
rownames(s)<-rownames(m)
y<-cbind("Others","Claudin")    //important to keep the rank of sfit
y<-cbind("Basal","Her2","LumB","LumA","Normal")
y<-cbind("ER-/HER2-","ER+/HER2- High Prolif","ER+/HER2- Low Prolif","HER2+")
y<-cbind("ER-/HER2-","ER+/HER2- High Prolif","ER+/HER2- Low Prolif","HER2+")
table(s$type)
for (k in 1:ncol(y)){
    kb=y[1,k]
    sb<-subset(s,type==kb)
    mb=m[(rownames(m)) %in% substr(gsub("\\.","-",rownames(sb)),1,12),]
    sfit <- survfit(Surv(year, five)~risk, data=mb)
    print(sfit)
}

data1 <- matrix(c(106,69,258,142,13,86,37,241,83,7), ncol=5, byrow=TRUE)
colnames(data1) <- c("Basal","Her2","LumB","LumA","Normal")
rownames(data1) <- c("low","high")
chisq.test(data1)