R/numericChrom.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 that checks if chrom is numeric, converts x/X and y/Y to 23 and 24 if not:

## Input:
### chrom: vector with chromosomes; numeric or character

## Output:
### chrom: numeric vector with chromosome numbers

## Required by:
### getArms
### checkSegments
### multipcf
### selectSegments
### selectData
### fastPcf
### pcf
### checkAndRetrievePlotInput
### plotFreq
### plotHeatmap
### plotWeightedFreq
### winsorize
### aspcf
### adjustSeg
### checkChrom

## Requires:
### none


numericChrom <- function(chrom) {
  if (!is.numeric(chrom)) {
    if (is.factor(chrom)) {
      # If chrom is factor; need to convert to character first
      chrom <- as.character(chrom)
    }
    # Replace X by 23:
    chrx <- c(which(chrom == "x"), which(chrom == "X"))
    chrom[chrx] <- 23
    # Replace Y by 24
    chry <- c(which(chrom == "y"), which(chrom == "Y"))
    chrom[chry] <- 24

    chrom <- as.numeric(chrom)
  }
  return(chrom)
}