这是我写的第二个版本。

#文件读函数
readfile_FPKM <- function(file_name){
  tmp <- read.table(file_name, header = T, sep = "\t", 
                    stringsAsFactors = F)[ , c("Gene.ID", "FPKM")]
  colnames(tmp) <- c("Gene.ID", strsplit(file_name, split = "[.]")[[1]][1])
  return(tmp)
}
readfile_TPM <- function(file_name){
  tmp <- read.table(file_name, header = T, sep = "\t", 
                    stringsAsFactors = F)[ , c("Gene.ID", "TPM")]
  colnames(tmp) <- c("Gene.ID", strsplit(file_name, split = "[.]")[[1]][1])
  return(tmp)
}
#读取文件
file <- dir()[grep(".tab", dir())]
data_FPKM <- lapply(file, readfile_FPKM)
data_TPM  <- lapply(file, readfile_TPM)

#把list中的数据合并到1个data.frame中  合并前需要去重
AllSample_FPKM <- data_FPKM[[1]]
for(i in 2:length(data_FPKM)){
  AllSample_FPKM <- merge(AllSample_FPKM,
                          data_FPKM[[i]][c(1,2)][!duplicated(data_FPKM[[i]][1]),], 
                          by = "Gene.ID")
                              }
AllSample_TPM <- data_TPM[[1]]
for(i in 2:length(data_TPM)){
  AllSample_TPM <- merge(AllSample_TPM,
                          data_TPM[[i]][c(1,2)][!duplicated(data_TPM[[i]][1]),], 
                          by = "Gene.ID")
}
rm(data_FPKM, data_TPM, i)
rm(data_TPM)

#数据归一化，计算每个样品FPKM值的和，让所有样品FPKM值的和均等比缩放到最大值
FPKM_Sum_Max <- max(apply(AllSample_FPKM[ ,c(-1,-2)],2, sum))
FPKM_Factor <- FPKM_Sum_Max/apply(AllSample_FPKM[ ,c(-1,-2)],2, sum)
AllSample_FPKM_scale <- sweep(AllSample_FPKM[,c(-1,-2)], 2, FPKM_Factor,'*')
AllSample_FPKM_scale <- cbind(AllSample_FPKM[ ,1:2], AllSample_FPKM_scale)
colnames(AllSample_FPKM_scale)[1] <- "Gene.ID"

TPM_Sum_Max <- max(apply(AllSample_TPM[ ,c(-1,-2)],2, sum))
TPM_Factor <- TPM_Sum_Max/apply(AllSample_TPM[ ,c(-1,-2)],2, sum)
AllSample_TPM_scale <- sweep(AllSample_TPM[,c(-1,-2)], 2, TPM_Factor,'*')
AllSample_TPM_scale <- cbind(AllSample_TPM[ ,1:2], AllSample_TPM_scale)
colnames(AllSample_TPM_scale)[1] <- "Gene.ID"

rm(FPKM_Factor,TPM_Factor,FPKM_Sum_Max, TPM_Sum_Max)

#整理数据
tmp <- read.table(file[1], header = T, sep = "\t", 
           stringsAsFactors = F)[ ,1:6]
AllSample_FPKM <- merge(tmp, AllSample_FPKM, by = "Gene.ID")
AllSample_FPKM_scale<- merge(tmp, AllSample_FPKM_scale, by = "Gene.ID")
AllSample_TPM <- merge(tmp, AllSample_TPM, by = "Gene.ID")
AllSample_TPM_scale<- merge(tmp, AllSample_TPM_scale, by = "Gene.ID")
rm(tmp)

#写文件
write.csv(AllSample_FPKM, "AllSample_FPKM.csv", row.names = F)
write.csv(AllSample_FPKM_scale, "AllSample_FPKM_scale.csv", row.names = F)
write.csv(AllSample_TPM, "AllSample_TPM.csv", row.names = F)
write.csv(AllSample_TPM_scale, "AllSample_TPM_scale.csv", row.names = F)

#清理
rm(list = ls())