ESITMATE 免疫评分

library(estimate)
estimate <- function(dat,pro){
  input.f=paste0(pro,'_estimate_input.txt')
  output.f=paste0(pro,'_estimate_gene.gct')
  output.ds=paste0(pro,'_estimate_score.gct')
  write.table(dat,file = input.f,sep = '\t',quote = F)
  library(estimate)
  filterCommonGenes(input.f=input.f,
                    output.f=output.f ,
                    id="GeneSymbol")
  estimateScore(input.ds = output.f,
                output.ds=output.ds,
                platform="illumina")   ## 注意platform
  scores=read.table(output.ds,skip = 2,header = T)
  rownames(scores)=scores[,1]
  scores=t(scores[,3:ncol(scores)])
  return(scores)
}
pro='PRCC'

#data<-read.table('data.txt',sep = '\t',check.names = F)
data[1:5,1:5]
scores2=estimate(data,pro)
head(scores2)
TumorPurity = cos(0.6049872018+0.0001467884 * scores2[,3])

scores=scores2
scores<-as.data.frame(scores)

scores%>%mutate(Purity=TumorPurity)->scores