该脚本适用于featureCounts数counts后的cpm和tpm计算
setwd("~/Desktop")#设置工作目录
countdata<-read.table("counts.txt",skip = 1,sep="\t",header = T,row.names = 1)
metadata <- countdata[,1:5]#提取基因信息count数据前的几列
countdata <- countdata[,6:ncol(countdata)]#提取counts数，counts数据主题部分
prefix<-"couts"#设置输出文件前缀名
cpm <- t(t(countdata)/colSums(countdata) * 1000000)#参考cpm定义
avg_cpm <- data.frame(avg_cpm=rowMeans(cpm))
#-----TPM Calculation------
kb <- metadata$Length / 1000
rpk <- countdata / kb
tpm <- t(t(rpk)/colSums(rpk) * 1000000)
avg_tpm <- data.frame(avg_tpm=rowMeans(tpm))
write.csv(avg_tpm,paste0(prefix,"_avg_tpm.csv"))
write.csv(avg_cpm,paste0(prefix,"_avg_cpm.csv"))
write.csv(tpm,paste0(prefix,"_tpm.csv"))
write.csv(cpm,paste0(prefix,"_cpm.csv"))
