R/getGlobPos.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 to covert local posistions to global positions based on a defined set of local stop positions chromosomes given in cyto.data

## Input:
### chromosomes: vector with chromosome numbers
### position: vector with positions
### pos.unit: positon's unit
### cyto.data: data frame with cytoband information
### delta: number of base pairs to add to end of each chromosome (used by plotCircle)

## Output:
### glob.pos: vector with global positions

## Required by:
### adjustSeg
### getx
### plotCircle

## Requires:
### getArmandChromStop



getGlobPos <- function(chromosomes, position, pos.unit, cyto.data, delta = 0) {
  # Get local stopping posistions for each p-arm and each chromosome from cytoband data
  l <- getArmandChromStop(cyto.data = cyto.data, unit = pos.unit)
  chromstop <- l$chromstop

  # Need to make sure that none of the input positions are larger than chromosome stop postions:
  u.chrom <- unique(chromosomes)
  new.pos <- position
  for (j in 1:length(u.chrom)) {
    probe.c <- chromosomes == u.chrom[j]
    # Check for positions that are larger than chromosome max position
    out <- which(position[probe.c] > chromstop[u.chrom[j]])
    # Replace these positions by max chrom position:
    new.pos[probe.c][out] <- chromstop[u.chrom[j]]
  }
  chromstop <- chromstop + delta
  glob.chromstop <- cumsum(chromstop) # Global stopping position for each chromosome

  glob.pos <- new.pos + c(0, glob.chromstop[-length(glob.chromstop)])[chromosomes] # Calculate global positions by adding global chromstop (for chrom > 1, for chrom=1 positions remain unchanged
  return(glob.pos)
} # end getGlobPos