19-等位基因突变的肿瘤异质性（mutant-allele tumor heterogeneity，MATH）分数计算

# setwd("G:/MedBioInfoCloud/analysis/TCGA/new/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/011-MATH/"
ifelse(dir.exists(opt),FALSE,dir.create(opt,recursive = T))

for(proj in project){
  message("===============================")
  message(proj)
  load(FilePath[grep(proj,FilePath)])#STARdata
  maf <- read.maf(snv,isTCGA=TRUE)
  #mutant-allele tumor heterogeneity
  barcode <- unique(maf@data$Tumor_Sample_Barcode)
  
  MATH <- data.frame()
  for (i in barcode){
    out.math = inferHeterogeneity(maf = maf, tsb = i)
    Tumor_Sample_Barcode <- unique(out.math$clusterData$Tumor_Sample_Barcode)
    m = unique(out.math$clusterData$MATH)
    out = data.frame(Tumor_Sample_Barcode, m)
    MATH = rbind(MATH, out)
  }
  save(MATH,file = paste0(opt,proj,"-MATH.Rdata"))
  
}