R/findPeaks.R

In adductomicsR: Processing of adductomic mass spectral datasets

#' identify peaks
#' @description identifies peaks in a vector of intensities.
#' @param x numeric vector of intensities.
#' @param m number of peaks to identify
#' @usage findPeaks(x, m = 3)
#' @return string of peaks
findPeaks <- function(x, m = 3) {
    diffts <- diff(x, na.pad = FALSE)
    shape <- diff(sign(diffts))
    pks <- vapply(
        which(shape < 0),
        FUN = function(i) {
            z <- i - m + 1
            z <- ifelse(z > 0, z, 1)
            w <- i + m + 1
            w <- ifelse(w < length(x), w, length(x))
            if (all(x[c(z:i, (i + 2):w)] <= x[i + 1]))
                return(i + 1)
            else
                return(numeric(0))
        },
        FUN.VALUE = numeric(1)
    )
    pks <- unlist(pks)
    pks
}  # end function