R/butterFilter.R

In NADfinder: Call wide peaks for sequencing data

#' Low pass filter on ratios by butterworth filter
#'
#' The Butterworth filter is a type of signal processing filter designed to
#' have as flat a frequency response as possible in the passband.
#'
#' @param ratios A vector of numeric. It is log2-transformed ratios,
#' CPMRatios or OddRatios in each window.
#' @param N numeric(1) or integer(1). 
#' Critical frequencies of the low pass filter will be set as 1/N.
#' 1/N is a cutoff at 1/N-th of the Nyquist frequency.
#' By default, it is suppose there are about 200 peaks in the inputs.
#'
#' @return A vector of numeric with same length of input ratios. 
#' The vector indicates smoothed ratios.
#'
#' @export
#' @importFrom signal butter filter
#' @importFrom stats loess.smooth
#' @examples
#' ratios <- runif(20000)
#' butterFilter(ratios)
#'
butterFilter <- function(ratios, N = ceiling(length(ratios) / 200))
{
    ## length(ratios) = chromosome length / step size
    ### Divide the chromosome into 200 regions
    stopifnot(inherits(ratios, c("numeric", "integer")))
    stopifnot(length(N) == 1)
    bf <- butter(2, 1 / N, type = "low")
    
    ## r2 filtered smoothed ratio
    r2 <- as.numeric(filter(bf, ratios))
    
    W1 <- floor(N / 2) + 1
    W2 <- N - W1
    ### the following loop is to shift the smoothed ratios half window backward
    if (length(r2) > N && W2 > 0)
    {
        y <- ratios[(length(r2) - W2):length(r2)]
        y[is.na(y)] <- min(y, na.rm = TRUE)
        c(r2[W1:length(r2)],
          loess.smooth(seq.int(W2 + 1), y,
                       evaluation = W2 + 1)$y)[seq_along(r2)]
    } else
    {
        r2
    }
}