R/construct.R

In jasenfinch/consensus: Consensus Structural Chemical Classifications for Putative Molecular Formula Assignments

#' Consensus structural classifications for a molecular formula
#' @description Generate a consensus structural classification for a molecular formula.
#' @param MF the molecular formula to search
#' @param db databases to search. Can be either `kegg` or `pubchem`.
#' @param organism the KEGG organism ID to search. Ignored if argument `db` includes `pubchem`.
#' @param adduct_rules_table a dataframe containing adduct formation rules. The defaults is `mzAnnotation::adduct_rules()`.
#' @param classyfireR_cache file path for a `classyfireR` cache. See the documentation of `classyfireR::get_classification` for more details.  
#' @return An S4 object of class `Consensus`.
#' @examples 
#' construct('C4H6O5')
#' @importFrom mzAnnotation adduct_rules
#' @importFrom methods new
#' @export

construct <- function(MF,
                      db = c('kegg','pubchem'),
                      organism = character(),
                      adduct_rules_table = adduct_rules(),
                      classyfireR_cache = NULL){
  
  db <- match.arg(
    db,
    c('kegg','pubchem'))
  
  if (db == 'pubchem') {
    organism <- character()
  }
  
  message(MF)
  
  x <- new('Consensus',
           MF = MF,
           database = db,
           organism = organism,
           adduct_rules = adduct_rules_table)
  
  x %>%
    mfHits() %>%
    classify(classyfireR_cache = classyfireR_cache) %>%
    pips() %>%
    calcConsensus()
}