From raw counts to TPM

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上篇文章提到了可以用TPMCalculator从bam file中直接计算TPM, 但是发现每个sample计算得到的基因数量不一样，没法进行下游visualization。所以这里提供另外一种方法 （R environment）

install.packages("DGEobj.utils")

library(DGEobj.utils)

Allgene <- read.csv("clipboard",header = TRUE,sep = "\t") #column1 is gene enzemble ID; column2 is geneLength

rownames(Allgene) <- Allgene$Geneid

allgeneexpression <- Allgene[,3:9]

geneLength <- Allgene$Length

tpmMatrix <- convertCounts(as.matrix(allgeneexpression),unit = "TPM",geneLength = geneLength,log = F,

normalize = "none",prior.count = NULL)

tpmMatrix1 <- as.data.frame(tpmMatrix) # 该data.frame可以继续进行下游分析。