R/findNN.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
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# Function that finds nearest non-missing neighbour

## Input:
# pos: a vector of positions
# obs: a logical vector indication which of the positions have observed copy number values

## Output:
# NNM: a vector which gives the nearest non-missing neighbour of the missing observations

## Required by:
### fastPcf
### pcf
### aspcf


## Requires:
### none


findNN <- function(pos, obs) {
  ind.obs <- which(obs)
  pos.obs <- pos[obs]
  pos.na <- pos[!obs]

  # Find distances between position of missing obs and positions of non-missing obs
  d <- sapply(pos.na, FUN = "-", y = pos.obs)
  if (!is.matrix(d)) {
    d <- matrix(d, nrow = length(pos.obs), ncol = length(pos.na))
  }
  d <- abs(d)
  nn <- apply(d, 2, which.min) # find which observed obs is the nearest
  nn <- ind.obs[nn] # get index for the nearest

  return(nn)
}