Transcriptome：counts转TPM

将counts数值转化为TPM

1、新建一个Rproject

将这些counts文件复制到Rproject目录下。

2、新建一个R程序

将下列代码复制其中。

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#清空当前环境中的所有变量
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rm(list = ls())
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# 定义 counts 表格所在的文件夹路径
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counts_folder <- "./Counts/"
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# 获取 counts 表格文件列表
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count_file <- list.files(counts_folder, pattern = "\\.txt$", full.names = TRUE)
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# 循环遍历每个 counts 表格进行转换
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for (count_file in count_file) {
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# 读取 featureCounts 结果文件
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counts_data <- read.table(count_file, header = TRUE, skip = 1)
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# 简化表头信息
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sample_name <- gsub("./Counts/","",sub("(.*)_hisat2.counts\\.txt", "\\1", count_file))
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names(counts_data)[ncol(counts_data)]<-sample_name
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# 提取基因长度信息
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gene_lengths <- counts_data$Length
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# 计算每个样本的总reads数
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sample_totals <- sum(counts_data[,ncol(counts_data)])
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# 计算 TPM
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tpm_data <- counts_data[, ncol(counts_data)] / (gene_lengths / 1000) / (sample_totals / 1e6)
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# 添加基因名列
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tpm_data <- cbind(counts_data[, 1], tpm_data)
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#对tpm_data文件表头进行重命名
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colnames(tpm_data)<-c("Geneid",paste0(gsub("_counts","",sample_name),"_tpm"))
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head(tpm_data)
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#定义输出文件名
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tpm_file <- gsub("_counts","",paste0("./TPM/",sample_name,"_tpm_output.txt"))
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# 将结果保存为 TPM 文件
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write.table(tpm_data, file = tpm_file, sep = "\t", 
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            quote = FALSE, col.names = TRUE, row.names = FALSE)
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}

3、合并TPM文件

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# 指定要合并的文件路径
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TPMs_folder <- "./TPM/"
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# 创建一个空的数据框用于存储合并结果
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merged_data <- data.frame()
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# 获取 TPMs 表格文件列表
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TPM_file <- list.files(TPMs_folder, pattern = "\\.txt$", full.names = TRUE)
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# 循环读取并合并文件
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for (TPM_file in TPM_file) {
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  # 读取当前文件
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  current_data <- read.table(TPM_file, header = TRUE, stringsAsFactors = FALSE)
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  # 判断是否为第一个文件，如果是，则直接赋值给合并结果
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  if (length(merged_data) == 0) {
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    merged_data <- current_data
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  } else {
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    # 合并当前文件到已有结果
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    merged_data <- merge(merged_data, current_data, by = "Geneid", all = TRUE)
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  }
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}
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# 输出合并结果
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write.table(merged_data, file = "all_TPM.txt", sep = "\t", 
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            quote = FALSE, col.names = TRUE, row.names = FALSE)

all_TPM.txt文件即为所有unique基因在各样本中的TPM表达量数值。