# ESTIMATE 计算免疫浸润得分

setwd(“/share/pub/zhangzc/COAD”)
input <- c(“TCGA_mRNA.txt”)
output <- c(“estimate_data.gct”)
filterCommonGenes(input.f=input,
output.f=output,
id=”GeneSymbol”)
score <- c(“TCGA_estimate_score.gct”)
estimateScore(input.ds = output,
output.ds=score,
platform=”illumina”)

scores=read.table(“TCGA_estimate_score.gct”,skip = 2,header = T)
rownames(scores)=scores[,1]
scores=t(scores[,3:ncol(scores)])
scores
write.table(scores,”TCGA_estimate_score.txt”,quote = F)