R语言计算tmb值

用户1359560

发布于 2020-12-16 18:03:32

4.3K0

tmb值与免疫检查点抑制剂疗效相关，而TCGA数据库中的tmb值可以通过TCGAmutations包来计算

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rm(list=ls())

setwd("D:\\SCIwork\\F25\\results\\tmb")
# BiocManager::install("PoisonAlien/TCGAmutations")
# TCGAmutations包整合了TCGA中全部样本的maf文件
# devtools::install_github(repo = "PoisonAlien/TCGAmutations")
library(TCGAmutations)

tmp=as.data.frame(tcga_available())

dt <- TCGAmutations::tcga_load(study = "KIRC")

dt <- dt@data

dt1 <- as.data.frame( table(dt$Tumor_Sample_Barcode))

names(dt1) <- c('Barcode', 'Freq')

dt1$tmb <- dt1$Freq/38

names(dt1)
 
 write.csv(dt1, file = 'KIRC_TMB.csv')