codeJG/checkDrugSynonym.R

In fcarazo/drughelper: Drug Identification and Drug Name Correction with Automatic Updates

source("./codeJG/formattingDrugName.R") 
source("./codeJG/downloadAbsentFile.R") 

checkDrugSynonym <- function(drugVector) {
  
  downloadAbsentFile()

  #DATAFRAME
  daf <- data.frame(x = character(),
                    Approved = character(),
                    DrugHelperID = character(),
                    Suggested.Synonym = character())
                        
  for (i in 1:length(drugVector)) {
    
          daf[i, 1] <- drugVector[i]
          
          DrugName <- formattingDrugName(drugVector[i])
          
          drugVector[i] <- DrugName #estas dos ultimas lineas tengo que mejorarlas,
          #si encuentra mas de una coincidencia, devuelve la primera, deberia
          #devolver la que mas se parezca, hacer prueba con "morphine"
          
          logicVector <- grepl(drugVector[i], datosChembl$synonyms_formatted)
          
          if (TRUE %in% logicVector){
            daf[i, 2] <- TRUE
          } else {
            daf[i, 2] <- FALSE
          }
        
    
    auxVectorsynonyms <- datosChembl$Drug[agrep(drugVector[i], datosChembl$synonyms_formatted, max.distance = 1)]
    auxTable <-datosChembl[agrep(drugVector[i], datosChembl$synonyms_formatted, max.distance = 1), ]
    
    tempDF = data.frame(Index = integer(), Synonyms = character())
    for (j in 1:length(auxVectorsynonyms)){
      
      list = unique(strsplit(auxTable$synonyms_formatted[j], split=";;;"))
      tempDF = rbind(tempDF, data.frame(Index = rownames(auxTable)[j], Synonyms = unlist(list)))
    }
    
    tempDF <- unique(tempDF)
    
    if (daf[i, 2] == TRUE) {
      daf[i, 3] <- auxTable$DrugHelper[rownames(datosChembl) == tempDF$Index[grep(paste0("^",drugVector[i],"$"), tempDF$Synonyms)[1]]]
      daf[i, 4] <- auxTable$Drug[rownames(datosChembl) == tempDF$Index[grep(paste0("^",drugVector[i],"$"), tempDF$Synonyms)[1]]]
    }
  }
  return(daf)
  
}