R/formula_filter.R

In EMSL-Computing/fticRanalysis: Analysis and visualization tools for FT-MS data

#' Formula filter object
#'
#' This function returns a formulaeFilt object for use with \code{\link{applyFilt}}
#' 
#' @param ftmsObj an object of the class 'peakData' or 'compoundData'
#'
#' @return Object of class 'formulaFilt' that contains the molecule identifier and whether a formula could be assigned or not. This can be used in conjunction with \code{\link{applyFilt}} to filter peaks without a formula assigned.
#'
#'
#' @author Lisa Bramer
#'
#' @export
#' @examples
#' data("examplePeakData")
#' filter_obj <- formula_filter(examplePeakData)
#' peakDataFiltered <- applyFilt(filter_obj, examplePeakData, remove="NoFormula")
formula_filter <- function(ftmsObj){
  
  # check that ftmsObj is of appropriate class #
  if(!inherits(ftmsObj,"peakData") & !inherits(ftmsObj, "compoundData")) stop("ftmsObj must be of class 'peakData' or 'compoundData'")
  
  edata_id = getEDataColName(ftmsObj)
  
  # determine whether a peak has a formula assigned or not #
  form_assigned = !is.na(ftmsObj$e_meta[,getMFColName(ftmsObj)])
  
  # output #
  output <- data.frame(ftmsObj$e_meta[, edata_id], form_assigned)
  names(output) <- c(edata_id, "Formula_Assigned")
  
  # reorder to match e_data:
  ind <- match(ftmsObj$e_data[, edata_id], output[, edata_id])
  output <- output[ind, ]
  
  orig_class <- class(output)
  class(output) <- c("formulaFilt", orig_class)
  
  return(output)
}