参考

简书 | 脚本 | R | 转录组 counts 2 tpm

  1.  # 导入包
  2. library(tidyverse)
  4. # 导入数据
  5. countsMatrix <- read_tsv("Counts.Length.tsv")
  7. # 宽变长，按样本分组，根据counts值和length计算tpm，长变宽
  8. tpmMatrix <- countsMatrix %>%
  9.   pivot_longer(c(-Geneids, -Length),
  10.                names_to = "Group",
  11.                values_to = "SampleCounts") %>%
  12.   group_by(Group) %>%
  13.   mutate(SampleTPM = (((SampleCounts/Length)*1e6)/sum(SampleCounts/Length))) %>%
  14.   pivot_wider(id_cols = "Geneids",
  15.               names_from = "Group",
  16.               values_from = "SampleTPM")
  18. # 导出tpm矩阵
  19. write_tsv(tpmMatrix, "TPM.tsv")