R/peakDet.R

In ATACseqQC: ATAC-seq Quality Control

#' Detect peak positions
#'
#' Detect the peaks positions and valley positions. The algorithm is modified
#' from github::dgromer/peakdet
#'
#' @param y A vector of numeric where to search peaks
#' @param delta A numeric of length 1, defining the local threshold
#' for peak detection. If it is set to 0, the delta will be set to
#' 1/10 of the range of y.
#' @param silence logical(1). 
#' If false, echo the delta value when delta is set as 0.
#'
#' @return A list with peakpos and valleypos. Both peakpos and valleypos are
#' vectors of numeric which indicate the positions of peak or valley.
#'

peakdet <- function(y, delta=0, silence=TRUE){
    peakpos <- NULL
    valleypos <- NULL
    stopifnot(delta>=0)
    if(delta==0){
        ry <- quantile(y, c(0, .25, .75, 1))[2:3]
        delta <- diff(ry)/10
        if(!silence){
            message("auto set delta = ", prettyNum(delta))
        }
    }
    minpos <- 1
    maxpos <- 1
    lookformax <- TRUE

    for(i in seq_along(y)){
        if (y[i] > y[maxpos]){
            maxpos <- i
        }
        if (y[i] < y[minpos]){
            minpos <- i
        }

        if (lookformax){
            if (y[i] < y[maxpos] - delta){
                peakpos <- c(peakpos, maxpos)
                minpos <- i
                lookformax <- FALSE
            }
        }else{
            if (y[i] > y[minpos] + delta){
                valleypos <- c(valleypos, minpos)
                maxpos <- i
                lookformax <- TRUE
            }
        }
    }

    list(peakpos = peakpos, valleypos = valleypos)
}