R/AuxFunctions.R

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

#' Drughelper Internal Functions
#'
#' @keywords internal
#' @name InternalFunctions
#' @import readr
#' @importFrom utils data
#' @return Internal outputs
#'

#' @rdname InternalFunctions
tsv2rdata <- function() {

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

  # DOWNLOAD RDATA FROM GITHUB
  # downloadAbsentFile(dir = tempdir())
  # dir <-  paste0(tempdir(),"\\datosChembl.RData")
  # datosChembl <- load(file = dir)
  # data("datosChembl")

  # DOWNLOADED FROM TSV
  requireNamespace("readr")
  datosChembl <- read_delim("https://raw.githubusercontent.com/jaaaviergarcia/drughelper/main/datosChembl.tsv",
                            "\t", escape_double = FALSE, trim_ws = TRUE)

  # singleDrugSynonymsChembl<-c()
  data("singleDrugSynonymsChembl", envir = environment())

  for (i in 1:nrow(datosChembl)){
    datosChembl$synonyms[i] <- toupper(datosChembl$synonyms[i])
  }

  datosChembl$synonymsChembl <- singleDrugSynonymsChembl$Drug_synonyms


  for (j in 1:nrow(datosChembl)){
    if (is.na(datosChembl$synonyms[j]))
      datosChembl$synonyms[j] <- datosChembl$synonymsChembl[j]
    else
      datosChembl$synonyms[j] <- paste(datosChembl$synonymsChembl[j], datosChembl$synonyms[j], sep=";;;")
  }

  datosChembl <- datosChembl[,-7]

  #UNIQUE SYNONYMS
  #vaux = vector auxiliar
  for (k in 1:nrow(datosChembl)){

    vaux <- strsplit(datosChembl$synonyms[k], ";;;")[[1]]
    vaux <- unique(vaux)
    datosChembl$synonyms[k] <- paste(vaux, collapse = ";;;")

  }

  # A continuacion el objetivo es llamar a la funcion ya
  # creada para que formatee la columna de sinonimos
  # (quitar espacios y signos de puntuación)

  source("../../codeJG/generateDB/formattingSynonymsTable.R")
  datosChembl <- updateTable(datosChembl)

  #Introducimos otras columnas como ids u otra información:

  datosChembl$DrugHelper <- paste0("DH0",1:nrow(datosChembl))

  #Ordenamos las columnas

  datosChembl <- subset(datosChembl, select = c(8,2,1,4,5,6,7,3))

  # save(datosChembl, file = "https://github.com/jaaaviergarcia/drughelper/datosChembl2.RData")
  # guardar esta tabla en github mediante codigo (esta guardada manualmente)
}



#' @rdname InternalFunctions
updateTable <- function(datosChembl){

  for (i in 1:nrow(datosChembl)){

    aux <- gsub("[[:blank:]]", "", datosChembl$synonyms[i])
    datosChembl$synonyms_formatted[i] <- gsub("[^[:alnum:];]", "", aux)

  }
  return(datosChembl)

}