计算基因表达量fpkm和tpm

简单粗暴，附上代码

 rate <- counts / lengths
 rate / sum(counts) * 1e9
 }



#----------------循环读入和写出---------
path='F:/matrix'#路径下全部是待处理的count文件
filename=dir(path)

for(i in 1:length(filename)){ 
    
    control1<-read.table(file=paste(path,filename[i],sep='/'),sep = "\t",col.names = c("gene_id","count"))
    control2<-read.table("F:/merge/gene1.length.txt",sep = "\t",col.names = c("gene_id","genelen"))#固定的
    count_len<-merge(control1,control2,by='gene_id')
    exprSet_rpkm=rpkm(count_len['count'],count_len['genelen'])
    exprSet_tpm=1e6*exprSet_rpkm/colSums(exprSet_rpkm)
    prefix<-filename[i]#设置输出文件前缀名
    
    
    final<- cbind(count_len['gene_id'],exprSet_tpm)
    write.csv(final,paste0(prefix,"_tpm.csv"),row.names=FALSE)
}