R/movingAverage.R

In RareVariantVis: A suite for analysis of rare genomic variants in whole genome sequencing data

movingAverage <- function(x, n=1, centered=FALSE) {

    # Function for moving average was adapted from Cookbook for R website by Winston Chang
    # http://www.cookbook-r.com/Manipulating_data/Calculating_a_moving_average/

    if (centered) {
        before <- floor  ((n-1)/2)
        after  <- ceiling((n-1)/2)
    } else {
        before <- n-1
        after  <- 0
    }

    # Track the sum and count of number of non-NA items
    s     <- rep(0, length(x))
    count <- rep(0, length(x))

    # Add the centered data
    new <- x
    # Add to count list wherever there isn't a
    count <- count + !is.na(new)
    # Now replace NA_s with 0_s and add to total
    new[is.na(new)] <- 0
    s <- s + new

    # Add the data from before
    i <- 1
    while (i <= before) {
        # This is the vector with offset values to add
        new   <- c(rep(NA, i), x[1:(length(x)-i)])

        count <- count + !is.na(new)
        new[is.na(new)] <- 0
        s <- s + new

        i <- i+1
    }

    # Add the data from after
    i <- 1
    while (i <= after) {
        # This is the vector with offset values to add
        new   <- c(x[(i+1):length(x)], rep(NA, i))

        count <- count + !is.na(new)
        new[is.na(new)] <- 0
        s <- s + new

        i <- i+1
    }

    # return sum divided by count
    s/count
}