R/medianFilter.r

In igordot/copynumber: Segmentation of single- and multi-track copy number data by penalized least squares regression (with hg38 and mm10).

####################################################################
## Author: Gro Nilsen, Knut Liestøl and Ole Christian Lingjærde.
## Maintainer: Gro Nilsen <gronilse@ifi.uio.no>
## License: Artistic 2.0
## Part of the copynumber package
## Reference: Nilsen and Liestøl et al. (2012), BMC Genomics
####################################################################


# Function to calculate running median for a given a window size

## Input:
### x: vector of numeric values
### k: window size to be used for the sliding window (actually half-window size)

## Output:
### runMedian : the running median corresponding to each observation

## Required by:
### getMad
### medianFilter


## Requires:
### none

medianFilter <- function(x, k) {
  n <- length(x)
  filtWidth <- 2 * k + 1

  # Make sure filtWidth does not exceed n
  if (filtWidth > n) {
    if (n == 0) {
      filtWidth <- 1
    } else if (n %% 2 == 0) {
      # runmed requires filtWidth to be odd, ensure this:
      filtWidth <- n - 1
    } else {
      filtWidth <- n
    }
  }

  runMedian <- runmed(x, k = filtWidth, endrule = "median")

  return(runMedian)
}