R/metClassUtil.R

In ncats/RaMP-DB: RaMP (Relational Database of Metabolomic Pathways)

#' Query to retrieve database ID prefixes for analyte types
#' @param analyteType value to indicate the desired analyte type. Value one of 'gene' or 'metabolite'
#' @return Returns list of database ID prefixes for selected 'gene' or 'metabolite'
#' @export  getPrefixesFromAnalytes
getPrefixesFromAnalytes<-function(db = RaMP(), analyteType="gene") {
  if (analyteType=="gene"){
    query1 <- "select distinct(IDtype) from source where geneOrCompound ='gene';"
    df1<- RaMP::runQuery(query1, db)
    df1 <- data.frame(analyteType="Genes/Proteins", idTypes=paste(df1$IDtype,collapse=", "))
    }
  else if (analyteType=="metabolite"){
    query2 <- "select distinct(IDtype) from source where geneOrCompound ='compound';"
    df1 <- RaMP::runQuery(query2, db)
    df1 <- data.frame(analyteType="Metabolites", idTypes=paste(df1$IDtype,collapse=", "))
    }
  else{
    print("analyteType must be 'gene' or 'metabolite'")
  }
  return(df1)
}


#' Returns class data sources for metabolites
#' @return Returns list of data sources for metabolites
getMetabClassDataSources<-function(db = RaMP()){
  query1<-"select distinct(source) from metabolite_class order by source asc"
  results<- RaMP::runQuery(query1, db)
  return(results)
}


#' Returns class categories for metabolites
#' @return Returns metabolite class types
#' @export getMetabClassTypes
getMetabClassTypes<-function(db = RaMP()){
  query1<-"select distinct(class_level_name) from metabolite_class order by class_level_name asc"
  results<- RaMP::runQuery(query1, db)
  return(results)
}

#' Returns chemical classes for classType
#' @param classType one of the metab class types as returned by getMetabClassTypes() function; if null
#' will return a list of available classes for each class type
#' @return Returns metabolite classes for classTypes
#' @export getMetabChemClass
getMetabChemClass <- function(db = RaMP(), classType= 'ClassyFire_super_class') {
  if (!is.null(classType)) {
    query1<- paste0("select class_level_name, class_name from metabolite_class where class_level_name = '",classType,"' group by class_level_name, class_name")
    res <- RaMP::runQuery(query1, db)
    res <- split(res$class_name,res$class_level_name)
  }

  else if (is.null(classType)){
    query1 <- "select class_level_name, class_name from metabolite_class group by class_level_name, class_name"
    res <- RaMP::runQuery(query1, db)
    res <- split(res$class_name,res$class_level_name)
  }

  if (length(res)==0){
    message(paste0(classType, ' Not Defined. Available Class Types:'))
    res<-getMetabClassTypes()

  }

  return(res)
}


#' Returns list of available ontologies from database
#' @return Returns ontologies listed in database
#' @export getOntologies

getOntologies <- function(db = RaMP()) {
  query1 <- "select * from ontology"
  OntoRes <- RaMP::runQuery(query1, db)
  return(OntoRes)
}