R/peakAsymmetry-method.R

In wilsontom/sRm: Toolkit for SRM-MS data (MS) data

#' Peak Asymmetry
#'
#' @rdname peakAsymmetry
#' @param object a SRM object
#' @return a `SRM` object
#'
#' @export


setMethod('peakAsymmetry', signature = 'SRM',
          function(object) {
            peakChromAsym <- list()

            for (i in 1:nrow(object@peaks)) {
            rawChrom <-
                object@chroms %>% dplyr::filter(
                  sampleID == object@peaks$sampleID[i] &
                    filter == object@peaks$filter[i] &
                    rt >= object@peaks$rtmin[i] &
                    rt <= object@peaks$rtmax[i]
                )

              rtmax <-
                max(rawChrom$rt[rawChrom$int == max(rawChrom$int)])

              peak_front_10 <-
                rawChrom$rt[rawChrom$rt < rtmax][which.min(abs(rawChrom$int[rawChrom$rt < rtmax] - max(rawChrom$int) * 0.1))]

              if(length(peak_front_10) == 0){
                peak_front_10 <- 0
              }

              peak_tail_10 <-
                rawChrom$rt[rawChrom$rt > rtmax][which.min(abs(rawChrom$int[rawChrom$rt > rtmax] - max(rawChrom$int) * 0.1))]

              if(length(peak_tail_10) == 0){
                peak_tail_10 <- 0
              }

              A10 <- rtmax - peak_front_10
              B10 <- peak_tail_10 - rtmax

              Asym <- B10 / A10

              peakChromAsym[[i]] <-
                object@peaks[i,] %>% dplyr::mutate(PeakAsymm = Asym)
            }

            object@peaks <- peakChromAsym %>% dplyr::bind_rows()

            return(object)

          })