R/getMad.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
####################################################################

# Get mad SD-estimate

## Input:
### x: vector of observations for which mad Sd is to be calculated
### k: window size to be used in median filtering

## Output:
### SD: mad sd estimate

## Required by:
### multipcf
### pcf
### aspcf


## Requires:
### medianFilter


getMad <- function(x, k = 25) {
  # Remove observations that are equal to zero; are likely to be imputed, should not contribute to sd:
  x <- x[x != 0]

  # Calculate runMedian
  runMedian <- medianFilter(x, k)

  dif <- x - runMedian
  SD <- mad(dif)

  return(SD)
}