R语言：人源基因ID转鼠源基因ID

最新推荐文章于 2024-05-20 11:34:51 发布

云淡风轻丷

最新推荐文章于 2024-05-20 11:34:51 发布

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本文链接：https://blog.csdn.net/qq_73470973/article/details/131919190

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方法一：

mouse_human_genes = read.csv("http://www.informatics.jax.org/downloads/reports/HOM_MouseHumanSequence.rpt",sep="\t")

convert_mouse_to_human <- function(gene_list){
  
  output = c()
  
  for(gene in gene_list){
    class_key = (mouse_human_genes %>% filter(Symbol == gene & Common.Organism.Name=="mouse, laboratory"))[['DB.Class.Key']]
    if(!identical(class_key, integer(0)) ){
      human_genes = (mouse_human_genes %>% filter(DB.Class.Key == class_key & Common.Organism.Name=="human"))[,"Symbol"]
      for(human_gene in human_genes){
        output = append(output,human_gene)
      }
    }
  }
  
  return (output)
}

方法二：

require("biomaRt")
human = useMart("ensembl", dataset = "hsapiens_gene_ensembl", host = "https://dec2021.archive.ensembl.org/")
mouse = useMart("ensembl", dataset = "mmusculus_gene_ensembl", host = "https://dec2021.archive.ensembl.org/")


genes = getLDS(attributes = c("mgi_symbol"), filters = "mgi_symbol", 
               values = a20$Row.names, 
               mart = mouse, 
               attributesL = c("hgnc_symbol"), 
               martL = human, uniqueRows=T)