数据库代码公开：泛癌免疫基因相关性分析

 
geneName = "MKI67"
data = read.table("Immunogene.txt", header=T, sep="\t", check.names=F)
data = as.matrix(data)
rownames(data) = data[,1]
data = data[,2:ncol(data)]
data = data[(data[,"Type"]=="Tumor"),]
Gene = read.table(singleGeneFile, header=T,sep="\t",row.names=1,check.names=F)
sameSample = intersect(row.names(Gene),row.names(data))
Gene = Gene[sameSample,]
data = data[sameSample,]
outTab = data.frame()
pTab = data.frame()
for(i in levels(factor(exp[,"CancerType"]))){
  data1 = data[(data[,"CancerType"] == i),]
  Gene1 = Gene[(Gene[,"CancerType"] == i),]
  x = as.numeric(Gene[,geneName])
  pVector = data.frame(i)
  outVector = data.frame(i)
  genes = colnames(data1)[2:(ncol(data1)-1)]
  for(j in genes){
    y = as.numeric(data1[,j])
    corT = cor.test(x,y,method="pearson")
    cor = corT$estimate
    pValue = corT$p.value
    pVector = cbind(pVector,pValue)
    outVector = cbind(outVector,cor)
  }
  pTab = rbind(pTab,pVector)
  outTab = rbind(outTab,outVector)
}
colNames = c("CancerType",colnames(data1)[2:(ncol(data1)-1)])
colnames(outTab) = colNames
write.table(outTab,file="Immunogene.cor.txt",sep="\t",row.names=F,quote=F)
colnames(pTab) = colNames
write.table(pTab,file="Immunogene.pval.txt",sep="\t",row.names=F,quote=F)