R/utils.R


#' Tidy EI spectrum
#' @description Converts MS-DIAL EI spectrum to data.frame
#' @param x spectrum to be converted
#' @importFrom stringr str_split_fixed
#' @return Returns EI spectrum as a \code{data.frame}.
#' @author Ethan Bass

tidy_eispectrum <- function(x){
  x<-str_split_fixed(strsplit(x,split = " ")[[1]], ":", 2)
  x <- apply(x,2,as.numeric)
  colnames(x) <- c("mz", "intensity")
  as.data.frame(x)
}

#' Find peak based on retention time and/or mass
#' @param x An \code{msdial_alignment} object
#' @param rt Retention time
#' @param mz Quant.mass
#' @param rt.tol Tolerance for matching retention time
#' @param mz.tol Tolerance for matching Quant.mass
#' @param plot_it Logical. Whether to plot the spectra.
#' @importFrom stringr str_split_fixed
#' @return Returns EI spectrum as a \code{data.frame}.
#' @author Ethan Bass
#' @export

find_peak <- function(x, rt, mz, rt.tol = .01, mz.tol =.05, plot_it = TRUE){
  pks <- seq_len(ncol(x$tab))
  if (!missing(rt)){
    pks1 <- which(abs(rt - as.numeric(x$peak_meta[,"Average.Rt.min."])) < rt.tol)
  } else{pks1 <- pks}
  if (!missing(mz)){
    pks2 <- which(abs(mz - as.numeric(x$peak_meta[,"Quant.mass"])) < mz.tol)
  } else{pks2 <- pks}
  pks <- intersect(pks1, pks2)
  if (plot_it)
    for (pk in pks){
      plot_spectrum(x, pk, type = "base")
    }
  pks
}