R/chromMax.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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# Get the maximum position on a given chromosome

# Input:
### chrom: number between 1-24 indicating which chromosome's ideogram is to be plotted
### cyto.data: data frame with cytoband-information
### unit: the unit used for positions in the plot
### cyto.unit: the unit used to represent positons in cyto.data

# Output:
### max.pos: a scalar giving the maximum position on this chromosome (given the cytoband information)

## Required by:
### plotFreq (chromosomeFreq)
### plotAllele
### plotChrom
### plotSample
### plotHeatmap
### plotWeightedFreq


## Requires:
### convert.unit


chromMax <- function(chrom, cyto.data, pos.unit, cyto.unit = "bp") {
  # Get scaling factor for positions
  s <- convert.unit(unit1 = pos.unit, unit2 = cyto.unit)

  # Get the rows in cytoband data that correspond to this chromosome
  if (chrom == 23) {
    txt <- "chrX"
  } else if (chrom == 24) {
    txt <- "chrY"
  } else {
    txt <- paste("chr", chrom, sep = "")
  }
  rows <- which(cyto.data[, 1] == txt)

  ## Get max position for this chromosome and scale according to pos.unit
  max.pos <- max(cyto.data[rows, 3])
  max.pos <- max.pos * s

  return(max.pos)
}