R/get_peak_info.R

In wilsontom/pickeR: Peak picking for low resolution liquid chromatography data

#' Get peak information
#'
#' Create a \code{peak_info} \code{data.frame}
#'
#' @param rt a numeric vector of retention time
#' @param int a numeric vector of intensity
#' @param peak_limits a \code{data.frame} indicating the left, right and apex indices for all detected peaks
#' @return a \code{peak_info} \code{data.frame}
#'
#' @author Tom Wilson \email{tpw2@@aber.ac.uk}

get_peak_info <- function(rt, int, peak_limits)
{
  # checks for rt int len and peak_limits return

  peak_info <-
    data.frame(matrix(nrow = nrow(peak_limits), ncol = 7))
  names(peak_info) <-
    c("peak_id",
      "rt",
      "rt_left",
      "rt_right",
      "int",
      "area",
      "peak_width")

  for (i in seq_along(1:nrow(peak_limits))) {
    peak_info[i, "peak_id"] <- i
    peak_info[i, "rt"] <- rt[peak_limits[i, "apex"]]
    peak_info[i, "int"] <- int[peak_limits[i, "apex"]]
    peak_info[i, "peak_width"] <-
      (rt[peak_limits[i, "right"]] * 60) - (rt[peak_limits[i, "left"]] * 60)

    peak_info[i, "rt_left"] <- rt[peak_limits[i, "left"]]
    peak_info[i, "rt_right"] <- rt[peak_limits[i, "right"]]

    peak_info[i, "area"] <-
      inegrate_peak(rt, int, c(peak_limits[i, "left"]:peak_limits[i, "right"]))
  }

  peak_info[, "rt"] <- round(peak_info[, "rt"], digits = 2)
  peak_info[, "rt_left"] <- round(peak_info[, "rt_left"], digits = 2)
  peak_info[, "rt_right"] <-
    round(peak_info[, "rt_right"], digits = 2)
  peak_info[, "peak_width"] <-
    round(peak_info[, "peak_width"], digits = 1)

  peak_info <-
    data.frame(peak_info,
               left = peak_limits[, "left"],
               apex = peak_limits[, "apex"],
               right = peak_limits[, "right"])
  return(peak_info)

}