18-肿瘤突变负荷（TMB）的计算

# setwd("H:/MedBioInfoCloud/analysis/TCGA/new/01-conventionalAnalysis")
options(stringsAsFactors = F)
library(TCGAbiolinks)
library(dplyr)
library(maftools)
FilePath <- dir("G:/MedBioInfoCloud/analysis/TCGA/new/processedTCGAdata/TCGA-SNV/",
                "SNV.Rdata$",full.names = T)

###TCGA数据库中33中癌症类型
project <- getGDCprojects()$project_id
project <- project[grep("TCGA-",project)]

opt <- "output/010-TMB/"
ifelse(dir.exists(opt),FALSE,dir.create(opt,recursive = T))

# proj <- "TCGA-LUAD"
for(proj in project){
  message("===============================")
  message(proj)
  load(FilePath[grep(proj,FilePath)])#STARdata
  maf <- read.maf(snv,isTCGA=TRUE)
  tmb <- tmb(maf = maf,
             captureSize = 50,
             logScale = T)
  save(tmb,file = paste0(opt,proj,"-TMB.Rdata"))
}