R/handleMissing.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
####################################################################

## Required by:
## pcf

## Requires:
## none


# find nearest non-missing neighbour, and add missing obs to segment where nearest neighbour is located
handleMissing <- function(nn, pos, obs, pos.start, pos.stop, seg.npos) {
  # find out which segment interval nn belongs to,
  inInt <- findInterval(pos[nn], pos.start)

  # add missing pos to number of pos in this segment
  seg.npos[unique(inInt)] <- as.vector(seg.npos[unique(inInt)] + table(inInt))

  # move segment start or stop if missing obs pos is smaller or larger than existing segment
  pos.na <- pos[!obs]
  t1 <- which(pos.na < pos.start[inInt])
  pos.start[inInt[t1]] <- pos.na[t1]
  t2 <- which(pos.na > pos.stop[inInt])
  pos.stop[inInt[t2]] <- pos.na[t2]

  return(list(pos.start = pos.start, pos.stop = pos.stop, seg.npos = seg.npos))
}