R/getArms.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 arm numbers from chromosomes, position and cytoband data:

## Input:
### chrom: vector of chromosome numbers
### pos: vector of positions
### pos.unit: unit for positions
### cyto.data: object specifying which genome assembly version should be used for cytoband data

## Output:
### arms: a character vector with arms; dentoed p and q

## Required by:
### adjustPos
### multipcf
### pcf
### winsorize
### aspcf


## Requires:
### getArmandChromStop
### numericChrom

getArms <- function(chrom, pos, pos.unit = "bp", cyto.data) {
  # Make sure chromosomes are numeric:
  chrom <- numericChrom(chrom)

  nProbe <- length(chrom)
  chrom.list <- unique(chrom)
  nChrom <- length(chrom.list)

  # Get local stopping posistions for each p-arm and each chromosome from cytoband data
  l <- getArmandChromStop(cyto.data = cyto.data, unit = pos.unit)
  pStop <- l$pstop
  chromStop <- l$chromstop

  # Intitialize
  arms <- rep(NA, nProbe)

  for (i in 1:nChrom) {
    # Find corresponding arm numbers:
    c <- chrom.list[i]
    ind.c <- which(chrom == c)

    arms[ind.c] <- "q"
    p.arm <- ind.c[pos[ind.c] <= pStop[c]]
    arms[p.arm] <- "p" # p-arm
  }

  return(arms)
}