R/spectra_format_converter.R

In MetabolomicsBasics: Basic Functions to Investigate Metabolomics Data Matrices

#' @title spectra_format_converter.
#' @description \code{spectra_format_converter} will generate a matrix with mz and int
#'   columns out of a text representation of a spectrum.
#' @details See examples.
#' @param txt Sample table.
#' @param m_prec Mass precision of output spectrum.
#' @param i_prec Intensity precision of output spectrum.
#' @return Matrix with mz and int columns.
#' @examples
#' spectra_format_converter(txt = "57.1:100 58.0001:10")
#' spectra_format_converter(txt = "58.0001:10 57.1:100", m_prec = 4)
#' @export
spectra_format_converter <- function(txt = NULL, m_prec = 3, i_prec = 0) {
  s <- plyr::ldply(strsplit(txt, " ")[[1]], function(x) {
    x <- strsplit(x, ":")[[1]]
    return(data.frame("mz" = as.numeric(x[1]), "int" = as.numeric(x[2])))
  })
  s <- as.matrix(s[order(s[, "mz"]), ])
  s[, 1] <- round(s[, 1], m_prec)
  s[, 2] <- round(s[, 2], i_prec)
  return(s)
}