R/diffGetPeaksIndex.R

In kbseah/mass2adduct: Mass Spectrometry Imaging Molecular Adduct Finder

#' Find pairs of mass peaks corresponding to a specific mass (report index)
#'
#' From a set of all possible mass pairs, find all pairs corresponding to a
#' specific mass difference, which might represent a molecular transformation
#' of interest.
#' 
#' @param diff massdiff; output from massdiff
#' @param by string; Subset the mass by mass difference (putative adduct
#'                   transformation) ("diff") or by parent ion ("parent")?
#' @param mass numeric; mass of putative adduct or parent ion in m/z units
#' @param width numeric; range of values to use
#'
#' @return subset of the original data frame d where the mass difference or
#'         parent ion is close to the specified mass of interest (within the
#'         specified width)

diffGetPeaksIndex <- function(diff, by=c("diff","parent"), mass=NULL, width=0.001) {
  if (is.null (mass)) {
    stop("Mass difference not specified")
  }
  diffLow <- mass - width/2
  diffUpp <- mass + width/2
  if (by[1] == "diff") {
    output <- which(diff$diff > diffLow & diff$diff <= diffUpp)
  } else if (by[1] == "parent") {
    output <- which(diff$A > diffLow & diff$A <= diffUpp)
  }
  return (output)
}