Rentrez package update symbol and get entrezID

#' Update_EntrezID_Officialsymbol_From_Symbol

#' 

#' This function is to get official symbol and entrezid using rentrez

#' For more information, please visit https://blog.naver.com/hyosil7979/220857307890

#' @param symbol (default=NULL) : symbol

#' @keywords genesymbol, entrez, official genesymbol, conversion

#' @export

#' @examples

#' Update_EntrezID_Officialsymbol_From_Symbol('P53')

 

Update_EntrezID_Officialsymbol_From_Symbol <-function(symbol){

  library(httr);library(curl);library(rentrez)

  #---- First: database[Gene], [TID]& [GENE]

  

  query1 <- paste("9606", "[TID] AND ", symbol, "[GENE]",sep="")

 

  res1 <- entrez_search(db="gene",  term=query1,retmax=1,version='2.0')

 

  cv1_1 <- tryCatch(entrez_summary(db="gene", id=res1$ids),error=function(e))

 

  cv1_2 <- as.vector(unlist(tryCatch(extract_from_esummary(cv1_1, c("name","uid")),error=function(e))))

 

  if(!is.null(cv1_2)& length(cv1_2)==2){

    

    mt1 <-c(symbol,cv1_2)

    

    return(mt1);

    

  }

 

  #---- Second: database[Gene], [TID]& [ALL]

  

  if(is.null(cv1_2)){

    

    query2 <- paste("9606", "[TID] AND ", symbol, "[ALL]",sep="")

    

    res2 <- entrez_search(db="gene",  term=query2,retmax=1)

    

    cv2_1 <- tryCatch(entrez_summary(db="gene", id=res2$ids),error=function(e))

    

    cv2_2 <- as.vector(unlist(tryCatch(extract_from_esummary(cv2_1, c("name","uid")),error=function(e))))

    

    if(!is.null(cv2_2)& length(cv2_2)==2){

      

      mt2 <-c(symbol,cv2_2)

      

      return(mt2);

      

    }

    

    #---- Third: database[Gene], [TID] & [ALL]

    

    if(is.null(cv2_2)){

      

      unigene.query <- paste("9606", "[TXID] AND ", symbol , "[ALL]",sep="")

      

      unigene.res2 <- entrez_search(db="unigene",  term=unigene.query,retmax=1)

      

      unigene.1 <- entrez_summary(db="unigene", id=unigene.res2$ids )

      

      unigene.2 <- as.vector(unlist(extract_from_esummary(unigene.1, c("gene"))))

      

      

      

      query3 <- paste("9606", "[TID] AND ", unigene.2, "[GENE]",sep="")

      

      res3 <- entrez_search(db="gene",  term=query3,retmax=1)

      

      cv3_1 <- entrez_summary(db="gene", id=res3$ids)

      

      cv3_2 <- as.vector(unlist(extract_from_esummary(cv3_1, c("name","uid"))))

      

      if(!is.null(cv3_2) & length(cv3_2)==2){

        

        mt3 <-c(symbol,cv3_2)

        

        return(mt3);

        

      }

    }

  }

}

# https://blog.naver.com/hyosil7979/220857307890

blog.naver.com/hyosil7979/220857307890

Update_EntrezID_Officialsymbol_From_Symbol.r

0.00MB