cuproptosis.mergeTime.R

[w28924461701]

#if (!requireNamespace("BiocManager", quietly = TRUE))

install.packages("BiocManager")

#BiocManager::install("limma")

library(limma) #引用包
lncFile="cuproptosisLncExp.txt" #cuproptosis相关lncRNA的表达文件
cliFile="time.txt" #生存数据文件
setwd("D:\easyHelper\148cuproptosis\13.mergeTime") #设置工作目录

#读取表达文件，并对输入文件整理
rt=read.table(lncFile, header=T, sep="\t", check.names=F)
rt=as.matrix(rt)
rownames(rt)=rt[,1]
exp=rt[,2:ncol(rt)]
dimnames=list(rownames(exp), colnames(exp))
data=matrix(as.numeric(as.matrix(exp)), nrow=nrow(exp), dimnames=dimnames)
data=avereps(data)

#删掉正常样品
group=sapply(strsplit(colnames(data),"\-"),"[",4)
group=sapply(strsplit(group,""),"[",1)
group=gsub("2","1",group)
data=data[,group==0]
colnames(data)=gsub("(.?)\-(.?)\-(.?)\-(.?)\-.*", "\1\-\2\-\3", colnames(data))
data=t(data)
data=avereps(data)

#读取生存数据
cli=read.csv('clipboard', header = TRUE, sep = "\t")
row.names(cli)<-cli$idd
cli$idd<-NULL
#数据合并并输出结果
sameSample=intersect(row.names(data),cli$idd)
data=data[sameSample,]
cli=cli[sameSample,]
out=cbind(cli,data)
out=cbind(id=row.names(out),out)
write.table(out,file="expTime.txt",sep="\t",row.names=F,quote=F)