R/DEGsGeneSymbol.R

In dming1024/TCGApackages0226: Analysis of TCGA data

#' Converting the ENSGID to GeneSymbol or Gene entrez ID
#'
#' use the DEGsGeneSymbol() fuction to get the DEGs based on DESeq2.
#' @rawNamespace import(biomaRt,except=select)
#' @param dataPath the direction of download Data
#' @export
#'
DEGsGeneSymbol<-function(dataPath){
  message("ENSGID在线注释，转换为genesymbol...",appendLF = F)
  load(file=".//output//step06.RData")
  #提取ensembleID
  #需要修改host
  ensemble=biomaRt::useMart("ensembl",
                            host="useast.ensembl.org")
  #查看有哪些可以用的dataset
  #listdatasets(ensemble)
  ensemble_selected=biomaRt::useDataset('hsapiens_gene_ensembl',mart = ensemble)
  #查看有哪些attributes
  #listattributes(ensemble_selected)
  #选择输出的属性（gene_id,symbol）
  #选择筛选的gene_id
  #选择待查的values
  pb <- progress::progress_bar$new()
  #pb$finished=FALSE
  ipo=biomaRt::getBM(attributes = c('ensembl_gene_id','hgnc_symbol'),
            filters = 'ensembl_gene_id',values = rownames(TCGA_result),mart = ensemble_selected)#对基因进行注释
  TCGA_result$ensembl_gene_id=rownames(TCGA_result)
  TCGA_result_genesymbol<-merge(as.data.frame(TCGA_result),ipo,by="ensembl_gene_id")
  write.csv(TCGA_result_genesymbol,".//output//step07_TCGA_analyis_results_with_geneSymbol.csv")
  save(TCGA_result_genesymbol,file = ".//output//step07.RData")
  message("Completed!")
}