R/generateMatrix.R

In dming1024/TCGApackages0226: Analysis of TCGA data

#' Generate the Gene Matrix of samples
#'
#' use the generateMatrix() fuction to orgnize the expression Matrix of Samples.
#' @import progress
#' @param dataPath the direction of download Data
#' @export
generateMatrix<-function(dataPath){
  setwd(dataPath)
  message("正在创建所有样本的基因表达矩阵...",appendLF = T)
  #定义空变量
  x_merge=NULL
  setwd(paste(dataPath,"all",sep="/"))
  file.remove(list.files(pattern = ".*.R"))
  i<-list.files()
  pb <- progress::progress_bar$new(total = length(i))
  try(
    for(n in i){
      x=read.delim(n,col.names = c('ID',substr(n,1,9)))
      if(is.null(x_merge)){
        x_merge=x
      }
      else{
        x_merge=merge(x_merge,x,by='ID')
      }
      pb$tick()
    }
  )

  setwd(dataPath)
  #head(x_merge)[,1:5]
  #基因转换成行名
  rownames(x_merge)<-x_merge$ID
  x_reduce=x_merge[-(1:5),]
  x_reduce=x_reduce[,-1]
  rownames(x_reduce)=x_merge$ID[-c(1:5)]
  #由于此步骤比较耗时，所以我将该步骤获得的x_reduce表达矩阵另存为Rdata文件
  save(x_reduce,file = ".//output//step02.RData")
  message("Completed!",appendLF = T)
}