R/getArmandChromStop.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 that finds p-arm and chromosome stopping positions based on cytoband information

## Input:
### cyto.data: dataframe with cytoband information
### unit: the unit used to represent positions in data to be plotted (bp,kbp,mbp)

## Output:
### pstop: a vector giving the stopping positions for each p-arm (adjusted to match unit)
### chromstop: a vector giving the stopping position for each chromosome (adjusted to match unit)

## Required by:
### getArms
### addChromlines
### getGlobPos
### getGlobal.xlim
### adjustSeg

## Requires : none

getArmandChromStop <- function(cyto.data, unit) {
  # Sort cyto.data by chromosome number; let be represented by X=23 and Y=24:
  chrom <- cyto.data[, 1]
  use.chrom <- gsub("chr", "", chrom) # Remove 'chr' from chrom-strings
  use.chrom[use.chrom == "X"] <- "23" # Replace X by 23
  use.chrom[use.chrom == "Y"] <- "24" # Replace Y by 24
  num.chrom <- as.numeric(use.chrom) # Convert to numeric chromosomes

  # Order such that chromosomes are in increasing order from 1:24:
  ord.chrom <- order(num.chrom)
  cyto.data <- cyto.data[ord.chrom, , drop = FALSE]

  # Get chromosome stopping positions:
  chrom <- cyto.data[, 1]
  chrom.stop <- which(chrom[1:length(chrom) - 1] != chrom[2:length(chrom)])
  chrom.stop <- c(chrom.stop, length(chrom)) # include last chromstop as well

  # Get p-arm stopping positions:
  arm.char <- substring(cyto.data[, 4], 1, 1) # Retrive first character in name which identifies p and q arms
  arm.stop <- which(arm.char[1:length(arm.char) - 1] != arm.char[2:length(arm.char)])
  p.stop <- arm.stop[-which(arm.stop %in% chrom.stop)] # Remove qstops

  pos.chromstop <- cyto.data[chrom.stop, 3] # Local stopping position for each chromosome
  pos.pstop <- cyto.data[p.stop, 3] # Local stopping position for each p-arm

  # Factor used to convert positions into desired unit
  f <- switch(unit,
    bp = 1,
    kbp = 10^(-3),
    mbp = 10^(-6)
  )

  return(list(pstop = pos.pstop * f, chromstop = pos.chromstop * f))
}