chipseeker2.R

library(clusterProfiler)

BiocManager::install("org.Hs.eg.db")
library(org.Hs.eg.db)
df<-read.table("exp_tumor2.txt")
dft<-t(df)
probe<-rownames(df)
ensg2entrez=toTable(org.Hs.egENSEMBL)
id= ensg2entrez[match(probe,ensg2entrez$ensembl_id),1]
annot=data.frame(probe=probe,"EntrezGene.ID"=id,"ENSEMBL"=probe)   
dft=dft[,!is.na(annot$EntrezGene.ID)]
annot=annot[!is.na(annot$EntrezGene.ID),] 
s<-molecular.subtyping(sbt.model="pam50",data=dft,annot=annot,do.mapping=TRUE)
str(s)
s=as.data.frame(s$subtype)
colnames(s)<-"type"
write.table(s,"subtype")