R: fast sliding window with given coordinates

Question

I have a data table with nrow being around a million or two and ncol of about 200.

Each entry in a row has a coordinate associated with it.

Tiny portion of the d

Answer 1

Rollapply works great with a small dataset. However, if you are working with several million rows (genomics) it is quite slow.

The following function is super fast:

data <- c(runif(100000, min=0, max=.1),runif(100000, min=.05, max=.1),runif(10000, min=.05, max=1), runif(100000, min=0, max=.2))
slideFunct <- function(data, window, step){
  total <- length(data)
  spots <- seq(from=1, to=(total-window), by=step)
  result <- vector(length = length(spots))
  for(i in 1:length(spots)){
    result[i] <- mean(data[spots[i]:(spots[i]+window)])
  }
  return(result)
}

Details here.